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Ketan Rohilla
Mar 8, 2022, 11:12:30 AM3/8/22
to gmx_MMPBSA
Hi,
I have centOS version 7. I am facing the following issue when running gmx_MMPBSA on my system. Kindly help me in this regard.
[INFO ] Checking external programs...
[ERROR ] MMPBSA_Error Could not find necessary program [cpptraj].Check the gmx_MMPBSA.log file to report the problem.
File "/root/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
app.make_prmtops()
File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 523, in make_prmtops
external_progs = utils.find_progs(self.INPUT, self.mpi_size) if self.master else {}
File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 654, in find_progs
GMXMMPBSA_ERROR('Could not find necessary program [%s]' % prog)
File "/root/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: Could not find necessary program [cpptraj]
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
Mario Sergio Valdes
Mar 8, 2022, 12:15:47 PM3/8/22
to gmx_MMPBSA
Did you install AmberTools? (conda install -c conda-forge ambertools compilers)
Ketan Rohilla
Mar 8, 2022, 11:39:35 PM3/8/22
to gmx_MMPBSA
Yes. I have installed AmberTools and also I have tried to install cpptraj separately but still it's not working.
Mario Sergio Valdes
Mar 8, 2022, 11:45:11 PM3/8/22
to gmx_MMPBSA
How is your work environment configured? That is, are you running gmx_MMPBSA on an HPC or a local machine? Show me an image of your terminal and the output of "echo $PATH", "which gmx_MMPBSA" and "which sander". Everything seems to indicate that the AmberTools bin directory is not being included in your Bach's profile.
Ketan Rohilla
Mar 9, 2022, 12:02:53 AM3/9/22
to gmx_MMPBSA
I am running gmx_MMPBSA on a HPC machine.
(base) [root@nmrmkp ~]# echo $PATH
/root/anaconda3/bin:/home/admin/anaconda3/envs/gmxMMPBSA/bin:/root/miniconda3/envs/gmxMMPBSA/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/usr/local/bin/g_mmpbsa:/root/bin
(base) [root@nmrmkp ~]# which gmx_MMPBSA
/root/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA
(base) [root@nmrmkp ~]# which sander
/root/anaconda3/bin/sander
/root/anaconda3/bin:/home/admin/anaconda3/envs/gmxMMPBSA/bin:/root/miniconda3/envs/gmxMMPBSA/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin:/usr/local/bin/g_mmpbsa:/root/bin
(base) [root@nmrmkp ~]# which gmx_MMPBSA
/root/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA
(base) [root@nmrmkp ~]# which sander
/root/anaconda3/bin/sander
Mario Sergio Valdes
Mar 9, 2022, 12:14:08 AM3/9/22
to gmx_MMPBSA
The problem is that you are running gmx_MMPBSA in its conda environment, which means that it is isolated from all other packages and environments. You have AmberTools installed in the base environment, so it is not found within the gmxMMPBSA environment. To do this you must install AmberTools within the same environment. If you follow the steps we show in the documentation it should work without problems (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/installation/)
Notes:
Notes:
- Currently, in the PATH variable, you have two environments of gmx_MMPBSA. This is because you have two miniconda/anaconda installed and active on the same bach profile. My recommendation is that you remove one so you don't have compatibility issues.
- To run gmx_MMPBSA you must have the environment in which it was installed active (conda activate gmxMMPBSA).
I look forward to your comments.
Mario S.
Ketan Rohilla
Mar 9, 2022, 2:48:05 AM3/9/22
to gmx_MMPBSA
actually, I am new to linux system. I followed the steps as shown in the documentation at first but it didn't work. After that I tried to install amber tools separately and messed things up. Now I couldn't find a way to get out of this problem.
I am executing the following command:
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 19 20 -ct no_pbc_1.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat
Mario Sergio Valdes
Mar 9, 2022, 3:24:48 AM3/9/22
to gmx_MMPBSA
Don't worry, we will help you.
First of all and most importantly, you shouldn't overwrite any system files, although I guess since it's an HPC it should have those limitations.
To carry out the successful installation of any program, you must first know what permissions and libraries it requires, as well as where to install it. In principle, gmx_MMPBSA is easy to install and does not require additional permissions.
You can do it one of two ways, by installing everything in a conda environment or by compiling AmberTools and then installing gmx_MMPBSA from pip.
If you want to compile AmberTools, you just have to do the following:
- Install the dependencies that are commented on the official page (https://ambermd.org/InstCentOS.php)
- Download the AmberTools zip and copy it to your home directory.
- Unzip it and follow the Amber installation instructions. In principle, it does not require elevated privileges so it should work correctly. Otherwise, run "./run_cmake && make install". This will make that "make install" run immediately after the previous command with no additional requirements.
- Make sure to add the source /path_to_install/amber.sh to your .bashrc. That way, whenever you open a new terminal, that command will load automatically.
- Lastly, install gmx_MMPBSA as described in the documentation for compiled AmberTools.
If you will install it using conda explicitly, then do the following:
- Remove the conda installation that you won't use, say the one in your home.
- Make sure you removed anything related to that installation from your .bashrc
- Follow the gmx_MMPBSA installation instructions for conda environments. Since an environment called gmxMMPBSA already exists, overwrite it.
You shouldn't have any problems if you follow these instructions.
Note that compiling AmberTools would cause the PYTHONPATH variable to be forcefully set, which could have compatibility issues with the currently active conda environment, ie /root/miniconda3 conda.
Note: Remember that every time you modify the .bashrc (it is hidden in your home /home/your_user/.bashrc), you must open a new terminal so that the profile you have modified is updated.
First of all and most importantly, you shouldn't overwrite any system files, although I guess since it's an HPC it should have those limitations.
To carry out the successful installation of any program, you must first know what permissions and libraries it requires, as well as where to install it. In principle, gmx_MMPBSA is easy to install and does not require additional permissions.
You can do it one of two ways, by installing everything in a conda environment or by compiling AmberTools and then installing gmx_MMPBSA from pip.
If you want to compile AmberTools, you just have to do the following:
- Install the dependencies that are commented on the official page (https://ambermd.org/InstCentOS.php)
- Download the AmberTools zip and copy it to your home directory.
- Unzip it and follow the Amber installation instructions. In principle, it does not require elevated privileges so it should work correctly. Otherwise, run "./run_cmake && make install". This will make that "make install" run immediately after the previous command with no additional requirements.
- Make sure to add the source /path_to_install/amber.sh to your .bashrc. That way, whenever you open a new terminal, that command will load automatically.
- Lastly, install gmx_MMPBSA as described in the documentation for compiled AmberTools.
If you will install it using conda explicitly, then do the following:
- Remove the conda installation that you won't use, say the one in your home.
- Make sure you removed anything related to that installation from your .bashrc
- Follow the gmx_MMPBSA installation instructions for conda environments. Since an environment called gmxMMPBSA already exists, overwrite it.
You shouldn't have any problems if you follow these instructions.
Note that compiling AmberTools would cause the PYTHONPATH variable to be forcefully set, which could have compatibility issues with the currently active conda environment, ie /root/miniconda3 conda.
Note: Remember that every time you modify the .bashrc (it is hidden in your home /home/your_user/.bashrc), you must open a new terminal so that the profile you have modified is updated.
If you're on Linux, you can use Krusader. This application is a very good file manager for beginners in handling, editing, and configuring HPC files. If I remember correctly, mobaxterm allows you to open files using whatever graphics server is available and supported. You can use them for editing the .bashrc file
If you have any other questions, I'd be happy to help.
HTH
HTH
Ketan Rohilla
Mar 9, 2022, 5:21:25 AM3/9/22
to gmx_MMPBSA
I tried to install gmx_MMPBSA on a local machine but the same error [cppraj] is coming.
/home/manoj/anaconda3/bin.AVX2_256:/home/manoj/anaconda3/envs/gmxMMPBSA/bin:/home/manoj/anaconda3/condabin:/home/manoj/.local/bin:/opt/OpenPrinting-Gutenprint/sbin:/opt/OpenPrinting-Gutenprint/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/spinev:/opt/intel/bin:/opt/spinev:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/intel/bin
(gmxMMPBSA) manoj@manoj:~/gmxmm$ which gmx_MMPBSA
/home/manoj/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA
(gmxMMPBSA) manoj@manoj:~/gmxmm$ which sander
/home/manoj/anaconda3/envs/gmxMMPBSA/bin/sander
Ketan Rohilla
Mar 9, 2022, 5:22:46 AM3/9/22
to gmx_MMPBSA
(gmxMMPBSA) manoj@manoj:~/gmxmm$ gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 18 19 -ct no_pbc_1.xtc -o FINAL_RESULTS_MMPBSA.dat
[INFO ] Starting gmx_MMPBSA v1.5.0.3
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 18 19 -ct no_pbc_1.xtc -o FINAL_RESULTS_MMPBSA.dat
[INFO ] Checking external programs...
[ERROR ] MMPBSA_Error Could not find necessary program [cpptraj].
Check the gmx_MMPBSA.log file to report the problem.
File "/home/manoj/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/manoj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
app.make_prmtops()
File "/home/manoj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 523, in make_prmtops
external_progs = utils.find_progs(self.INPUT, self.mpi_size) if self.master else {}
File "/home/manoj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 654, in find_progs
GMXMMPBSA_ERROR('Could not find necessary program [%s]' % prog)
File "/home/manoj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: Could not find necessary program [cpptraj]
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
[INFO ] Starting gmx_MMPBSA v1.5.0.3
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 18 19 -ct no_pbc_1.xtc -o FINAL_RESULTS_MMPBSA.dat
[INFO ] Checking external programs...
[ERROR ] MMPBSA_Error Could not find necessary program [cpptraj].
Check the gmx_MMPBSA.log file to report the problem.
sys.exit(gmxmmpbsa())
File "/home/manoj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
app.make_prmtops()
File "/home/manoj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 523, in make_prmtops
external_progs = utils.find_progs(self.INPUT, self.mpi_size) if self.master else {}
GMXMMPBSA_ERROR('Could not find necessary program [%s]' % prog)
raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: Could not find necessary program [cpptraj]
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
Mario Sergio Valdes
Mar 9, 2022, 11:37:44 AM3/9/22
to gmx_MMPBSA
Please, show me the output of conda list in gmxMMPBSA environment
Ketan Rohilla
Mar 9, 2022, 11:49:47 PM3/9/22
to gmx_MMPBSA
(gmxMMPBSA) manoj@manoj:~/gmxmm$ conda list
# packages in environment at /home/manoj/anaconda3/envs/gmxMMPBSA:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
amberlite 16.0 pypi_0 pypi
ambertools 21.9 py39h69e27f8_0 conda-forge
amberutils 21.0 pypi_0 pypi
arpack 3.7.0 hdefa2d7_2 conda-forge
binutils 2.36.1 hdd6e379_2 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_6 conda-forge
boost-cpp 1.74.0 h6cacc03_7 conda-forge
brotli 1.0.9 h7f98852_6 conda-forge
brotli-bin 1.0.9 h7f98852_6 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-compiler 1.4.1 h166bdaf_0 conda-forge
ca-certificates 2020.10.14 0 anaconda
certifi 2021.10.8 py39hf3d152e_1 conda-forge
compilers 1.4.1 ha770c72_0 conda-forge
curl 7.82.0 h2283fc2_0 conda-forge
cxx-compiler 1.4.1 h924138e_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.28 py39he80948d_0 conda-forge
expat 2.4.7 h27087fc_0 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
fonttools 4.29.1 py39h3811e60_0 conda-forge
fortran-compiler 1.4.1 h2a4ca65_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
gcc 10.3.0 he2824d0_6 conda-forge
gcc_impl_linux-64 10.3.0 hf2f2afa_13 conda-forge
gcc_linux-64 10.3.0 hc39de41_6 conda-forge
gettext 0.19.8.1 h9b4dc7a_1 anaconda
gfortran 10.3.0 h18518b4_6 conda-forge
gfortran_impl_linux-64 10.3.0 h73f4979_13 conda-forge
gfortran_linux-64 10.3.0 hb09a455_6 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
git 2.35.1 pl5321h04cb727_0 conda-forge
gmx-mmpbsa 1.5.0.3 pypi_0 pypi
gxx 10.3.0 he2824d0_6 conda-forge
gxx_impl_linux-64 10.3.0 hf2f2afa_13 conda-forge
gxx_linux-64 10.3.0 h2593f52_6 conda-forge
h5py 3.6.0 pypi_0 pypi
hdf4 4.2.15 h10796ff_3 conda-forge
hdf5 1.12.1 nompi_h4df4325_104 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9e h7f98852_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.3.2 py39h1a9c180_1 conda-forge
krb5 1.19.2 h08a2579_4 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h7f98852_6 conda-forge
libbrotlidec 1.0.9 h7f98852_6 conda-forge
libbrotlienc 1.0.9 h7f98852_6 conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcurl 7.82.0 h2283fc2_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 10.3.0 he6cfe16_13 conda-forge
libgcc-ng 11.2.0 h1d223b6_13 conda-forge
libgfortran-ng 11.2.0 h69a702a_13 conda-forge
libgfortran5 11.2.0 h5c6108e_13 conda-forge
libgomp 11.2.0 h1d223b6_13 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnetcdf 4.8.1 nompi_hb3fd0d9_101 conda-forge
libnghttp2 1.47.0 he49606f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libsanitizer 10.3.0 h26c7422_13 conda-forge
libssh2 1.10.0 ha35d2d1_2 conda-forge
libstdcxx-devel_linux-64 10.3.0 he6cfe16_13 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_13 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libzip 1.8.0 h1c5bbd1_1 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
matplotlib-base 3.5.1 py39h2fa2bec_0 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mpi 1.0 openmpi conda-forge
mpi4py 3.1.3 py39hc649577_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.3 h9c3ff4c_0 conda-forge
netcdf-fortran 4.5.4 nompi_h2b6e579_100 conda-forge
numpy 1.22.3 py39h18676bf_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openmpi 4.1.2 hbfc84c5_0 conda-forge
openssl 3.0.0 h7f98852_2 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.1rc0 pypi_0 pypi
pandas 1.4.1 py39hde0f152_0 conda-forge
parmed 3.4.3+5.g16fb236 pypi_0 pypi
pcre2 10.37 h032f7d1_0 conda-forge
pdb4amber 20.1 pypi_0 pypi
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.0.1 py39hae2aec6_2 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyqt5 5.15.6 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.9.1 pypi_0 pypi
python 3.9.10 hc74c709_2_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2021.3 pyhd8ed1ab_0 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
sander 16.0 pypi_0 pypi
scipy 1.8.0 py39hee8e79c_1 conda-forge
seaborn 0.11.2 pypi_0 pypi
setuptools 60.9.3 py39hf3d152e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.37.0 h9cd32fc_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2021e he74cb21_0 conda-forge
unicodedata2 14.0.0 py39h3811e60_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
# packages in environment at /home/manoj/anaconda3/envs/gmxMMPBSA:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
amberlite 16.0 pypi_0 pypi
ambertools 21.9 py39h69e27f8_0 conda-forge
amberutils 21.0 pypi_0 pypi
arpack 3.7.0 hdefa2d7_2 conda-forge
binutils 2.36.1 hdd6e379_2 conda-forge
binutils_impl_linux-64 2.36.1 h193b22a_2 conda-forge
binutils_linux-64 2.36 hf3e587d_6 conda-forge
boost-cpp 1.74.0 h6cacc03_7 conda-forge
brotli 1.0.9 h7f98852_6 conda-forge
brotli-bin 1.0.9 h7f98852_6 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-compiler 1.4.1 h166bdaf_0 conda-forge
ca-certificates 2020.10.14 0 anaconda
certifi 2021.10.8 py39hf3d152e_1 conda-forge
compilers 1.4.1 ha770c72_0 conda-forge
curl 7.82.0 h2283fc2_0 conda-forge
cxx-compiler 1.4.1 h924138e_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.28 py39he80948d_0 conda-forge
expat 2.4.7 h27087fc_0 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
fonttools 4.29.1 py39h3811e60_0 conda-forge
fortran-compiler 1.4.1 h2a4ca65_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
gcc 10.3.0 he2824d0_6 conda-forge
gcc_impl_linux-64 10.3.0 hf2f2afa_13 conda-forge
gcc_linux-64 10.3.0 hc39de41_6 conda-forge
gettext 0.19.8.1 h9b4dc7a_1 anaconda
gfortran 10.3.0 h18518b4_6 conda-forge
gfortran_impl_linux-64 10.3.0 h73f4979_13 conda-forge
gfortran_linux-64 10.3.0 hb09a455_6 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
git 2.35.1 pl5321h04cb727_0 conda-forge
gmx-mmpbsa 1.5.0.3 pypi_0 pypi
gxx 10.3.0 he2824d0_6 conda-forge
gxx_impl_linux-64 10.3.0 hf2f2afa_13 conda-forge
gxx_linux-64 10.3.0 h2593f52_6 conda-forge
h5py 3.6.0 pypi_0 pypi
hdf4 4.2.15 h10796ff_3 conda-forge
hdf5 1.12.1 nompi_h4df4325_104 conda-forge
icu 69.1 h9c3ff4c_0 conda-forge
jbig 2.1 h7f98852_2003 conda-forge
jpeg 9e h7f98852_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.3.2 py39h1a9c180_1 conda-forge
krb5 1.19.2 h08a2579_4 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h7f98852_6 conda-forge
libbrotlidec 1.0.9 h7f98852_6 conda-forge
libbrotlienc 1.0.9 h7f98852_6 conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcurl 7.82.0 h2283fc2_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-devel_linux-64 10.3.0 he6cfe16_13 conda-forge
libgcc-ng 11.2.0 h1d223b6_13 conda-forge
libgfortran-ng 11.2.0 h69a702a_13 conda-forge
libgfortran5 11.2.0 h5c6108e_13 conda-forge
libgomp 11.2.0 h1d223b6_13 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnetcdf 4.8.1 nompi_hb3fd0d9_101 conda-forge
libnghttp2 1.47.0 he49606f_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.18 pthreads_h8fe5266_0 conda-forge
libpng 1.6.37 h21135ba_2 conda-forge
libsanitizer 10.3.0 h26c7422_13 conda-forge
libssh2 1.10.0 ha35d2d1_2 conda-forge
libstdcxx-devel_linux-64 10.3.0 he6cfe16_13 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_13 conda-forge
libtiff 4.3.0 h542a066_3 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libwebp 1.2.2 h3452ae3_0 conda-forge
libwebp-base 1.2.2 h7f98852_1 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libzip 1.8.0 h1c5bbd1_1 conda-forge
libzlib 1.2.11 h36c2ea0_1013 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
matplotlib-base 3.5.1 py39h2fa2bec_0 conda-forge
mmpbsa-py 16.0 pypi_0 pypi
mpi 1.0 openmpi conda-forge
mpi4py 3.1.3 py39hc649577_0 conda-forge
munkres 1.1.4 pyh9f0ad1d_0 conda-forge
ncurses 6.3 h9c3ff4c_0 conda-forge
netcdf-fortran 4.5.4 nompi_h2b6e579_100 conda-forge
numpy 1.22.3 py39h18676bf_0 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openmpi 4.1.2 hbfc84c5_0 conda-forge
openssl 3.0.0 h7f98852_2 conda-forge
packaging 21.3 pyhd8ed1ab_0 conda-forge
packmol 20.010 h86c2bf4_0 conda-forge
packmol-memgen 1.2.1rc0 pypi_0 pypi
pandas 1.4.1 py39hde0f152_0 conda-forge
parmed 3.4.3+5.g16fb236 pypi_0 pypi
pcre2 10.37 h032f7d1_0 conda-forge
pdb4amber 20.1 pypi_0 pypi
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.0.1 py39hae2aec6_2 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyparsing 3.0.7 pyhd8ed1ab_0 conda-forge
pyqt5 5.15.6 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.9.1 pypi_0 pypi
python 3.9.10 hc74c709_2_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python_abi 3.9 2_cp39 conda-forge
pytraj 2.0.6 pypi_0 pypi
pytz 2021.3 pyhd8ed1ab_0 conda-forge
readline 8.1 h46c0cb4_0 conda-forge
sander 16.0 pypi_0 pypi
scipy 1.8.0 py39hee8e79c_1 conda-forge
seaborn 0.11.2 pypi_0 pypi
setuptools 60.9.3 py39hf3d152e_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.37.0 h9cd32fc_0 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tzdata 2021e he74cb21_0 conda-forge
unicodedata2 14.0.0 py39h3811e60_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.7.2 h7f98852_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h7f98852_1 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-xextproto 7.3.0 h7f98852_1002 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.5 h516909a_1 conda-forge
zlib 1.2.11 h36c2ea0_1013 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
Ketan Rohilla
Mar 9, 2022, 11:57:46 PM3/9/22
to gmx_MMPBSA
Also, cpptraj command is running as a standalone command.
(gmxMMPBSA) manoj@manoj:~/gmxmm$ cpptraj
CPPTRAJ: Trajectory Analysis. V5.1.0
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 03/10/22 10:26:34
| Available memory: 43.218 GB
(gmxMMPBSA) manoj@manoj:~/gmxmm$ cpptraj
CPPTRAJ: Trajectory Analysis. V5.1.0
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 03/10/22 10:26:34
| Available memory: 43.218 GB
Mario Ernesto
Mar 10, 2022, 12:02:17 AM3/10/22
to Ketan Rohilla, gmx_MMPBSA
could you please show us teh output of this command in the terminal:
which cpptraj
cheers!
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Ketan Rohilla
Mar 10, 2022, 12:05:10 AM3/10/22
to gmx_MMPBSA
(gmxMMPBSA) manoj@manoj:~/gmxmm$ which cpptraj
/home/manoj/anaconda3/envs/gmxMMPBSA/bin/cpptraj
/home/manoj/anaconda3/envs/gmxMMPBSA/bin/cpptraj
Mario Sergio Valdes
Mar 10, 2022, 12:26:16 AM3/10/22
to gmx_MMPBSA
This is rare. The only thing that occurs to me is that the shutil module is not working correctly on Centos7. Please run these commands and show me the output.
python
import shutil, os
shutil.which('cpptraj', path=os.environ['PATH'])
python
import shutil, os
shutil.which('cpptraj', path=os.environ['PATH'])
Ketan Rohilla
Mar 10, 2022, 1:44:44 AM3/10/22
to gmx_MMPBSA
(gmxMMPBSA) manoj@manoj:~/gmxmm$ python
Python 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:24:37)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import shutil, os
>>> shutil.which('cpptraj', path=os.environ['PATH'])
'/home/manoj/anaconda3/envs/gmxMMPBSA/bin/cpptraj'
Python 3.9.10 | packaged by conda-forge | (main, Feb 1 2022, 21:24:37)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import shutil, os
>>> shutil.which('cpptraj', path=os.environ['PATH'])
Mario Sergio Valdes
Mar 10, 2022, 1:47:48 AM3/10/22
to gmx_MMPBSA
Are you defining the gmx_path variable in the input file?
Ketan Rohilla
Mar 10, 2022, 2:00:16 AM3/10/22
to gmx_MMPBSA
these are my input files input file and the command I am executing:
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 18 19 -ct no_pbc_1.xtc -o FINAL_RESULTS_MMPBSA.dat
Mario Sergio Valdes
Mar 10, 2022, 2:09:46 AM3/10/22
to gmx_MMPBSA
Ok, it's a bug. I have already solved it. Update gmx_MMPBSA from GitHub (python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA) and tell me if the problem is solved
Note: The gmx_path variable accepts only the Gromacs bin folder. That is, the value of this variable must be the folder where the Gromacs executable(s) are located, for example, /home/mario/gromacs/bin. You must not define the executable explicitly
Shiv Bharadwaj
Mar 10, 2022, 3:00:04 AM3/10/22
to Mario Sergio Valdes, gmx_MMPBSA
Hello may be its helpful!
conda create -n gmxMMPBSA python=3.9 -y -q
Create gmxMMPBSA environment
conda activate gmxMMPBSA
conda install -c conda-forge mpi4py ambertools=21 -y -q
python -m pip install gmx-mmpbsa
Create gmxMMPBSA environment
conda activate gmxMMPBSA
conda install -c conda-forge mpi4py ambertools=21 -y -q
python -m pip install gmx-mmpbsa
If this shows anyerror? Make new new env; for example gmxMMPBSA2
conda install -c conda-forge mpi4py ambertools=21 -y -q
python -m pip install gmx-mmpbsa
python -m pip install gmx-mmpbsa
And gmx-mmpbsa test 1
And it worked for me on ubuntu!
But make sure you install all the package in first env and then it should work!
Shiv
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/e64b38b1-7617-479c-bddc-e2fc30b31ef2n%40googlegroups.com.
Mario Sergio Valdes
Mar 10, 2022, 4:11:45 AM3/10/22
to gmx_MMPBSA
Thanks, Shiv. However, it is a bug that I already fixed. When the gmx_path variable was defined, only that path was used and the PATH variable was ignored. You should have no problems with the installation mode that we describe in the documentation. We tested it on various Linux-based OS and all works fine.
Sincerely
Mario S.
Ketan Rohilla
Mar 10, 2022, 6:02:33 AM3/10/22
to gmx_MMPBSA
Thanks Mario,
(gmxMMPBSA) [root@nmrmkp mmpbsaTEST]# gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 19 20 -ct no_pbc_1.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat
[INFO ] Starting gmx_MMPBSA v1.5.0.3+37.g67bd79a
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 19 20 -ct no_pbc_1.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat
Check the gmx_MMPBSA.log file to report the problem.
raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
that cpptraj error is reolved now. But now I am facing the following error:
(gmxMMPBSA) [root@nmrmkp mmpbsaTEST]# gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 19 20 -ct no_pbc_1.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat
[INFO ] Starting gmx_MMPBSA v1.5.0.3+37.g67bd79a
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ci insulin-protamine.ndx -cg 19 20 -ct no_pbc_1.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /root/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /root/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /root/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /root/gromacs-2020.6/build/bin/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group 19_20 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error /root/gromacs-2020.6/build/bin/gmx trjconv failed when querying no_pbc_1.xtc.
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /root/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /root/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /root/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /root/gromacs-2020.6/build/bin/gmx
[INFO ] Checking external programs...Done.
[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Normal Complex: Saving group 19_20 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[ERROR ] MMPBSA_Error /root/gromacs-2020.6/build/bin/gmx trjconv failed when querying no_pbc_1.xtc.
Check the gmx_MMPBSA.log file to report the problem.
File "/root/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
app.make_prmtops()
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 533, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
self.gmx2pdb()
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 259, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
sys.exit(gmxmmpbsa())
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
app.make_prmtops()
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 533, in make_prmtops
self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 116, in buildTopology
self.gmx2pdb()
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 259, in gmx2pdb
GMXMMPBSA_ERROR('%s failed when querying %s' % (' '.join(comprog), self.FILES.complex_trajs[0]))
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 169, in __init__
raise exc(msg + '\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: /root/gromacs-2020.6/build/bin/gmx trjconv failed when querying no_pbc_1.xtc
Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.
Mario Ernesto
Mar 10, 2022, 10:36:55 AM3/10/22
to Ketan Rohilla, gmx_MMPBSA
Could you please send us the gmx_MMPBSA.log file!?
To view this discussion on the web visit https://groups.google.com/d/msgid/gmx_mmpbsa/81cde4aa-6f41-4468-8176-90a65a2f6a89n%40googlegroups.com.
Ketan Rohilla
Mar 10, 2022, 11:32:40 PM3/10/22
to gmx_MMPBSA
Its working now on UBUNTU system but its showing following error now:
ImportError: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /home/manoj/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/scipy/linalg/_matfuncs_sqrtm_triu.cpython-39-x86_64-linux-gnu.so)
Aborted (core dumped)
Aborted (core dumped)
Mario Sergio Valdes
Mar 10, 2022, 11:45:12 PM3/10/22
to gmx_MMPBSA
Are you using a version less than 18.04? This problem has already been reported. Run the instructions I mention here (https://groups.google.com/g/gmx_mmpbsa/c/lbbjvewEJi4/m/pYKIotm7CAAJ)
Please note that these older versions are no longer officially supported by us as we have too many versions to test and we don't have enough time.
HTH!
Mario S.
Ketan Rohilla
Mar 10, 2022, 11:52:02 PM3/10/22
to gmx_MMPBSA
My ubuntu version is as follows.. Should I use the above-mentioned commands to solve the problem for this version also?
LSB Version: core-9.20170808ubuntu1-noarch:printing-9.20170808ubuntu1-noarch:security-9.20170808ubuntu1-noarch
Distributor ID: Ubuntu
Description: Ubuntu 18.04.6 LTS
Release: 18.04
Codename: bionic
Mario Sergio Valdes
Mar 10, 2022, 11:54:53 PM3/10/22
to gmx_MMPBSA
Yes, check that the GLIBCXX version >= 3.4.26... The instructions I describe should upgrade the GLIBCXX version to 3.4.28 or higher
Ketan Rohilla
Mar 11, 2022, 12:58:46 AM3/11/22
to gmx_MMPBSA
What should I do now?
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package gcc-4.9 is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
E: Package 'gcc-4.9' has no installation candidate
Mario Sergio Valdes
Mar 11, 2022, 1:09:48 AM3/11/22
to gmx_MMPBSA
Did you follow these instructions?
Check the supported versions again
strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
Add this repo and update the libstdc++6 library
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt update
sudo apt install gcc-4.9
sudo apt install upgrade libstdc++6
sudo apt update
sudo apt install gcc-4.9
sudo apt install upgrade libstdc++6
Check the supported versions again
strings/usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
?
Ketan Rohilla
Mar 11, 2022, 1:49:45 AM3/11/22
to gmx_MMPBSA
Yes. I followed the same commands. First command is showing the following result:
GLIBCXX_3.4
GLIBCXX_3.4.1
GLIBCXX_3.4.2
GLIBCXX_3.4.3
GLIBCXX_3.4.4
GLIBCXX_3.4.5
GLIBCXX_3.4.6
GLIBCXX_3.4.7
GLIBCXX_3.4.8
GLIBCXX_3.4.9
GLIBCXX_3.4.10
GLIBCXX_3.4.11
GLIBCXX_3.4.12
GLIBCXX_3.4.13
GLIBCXX_3.4.14
GLIBCXX_3.4.15
GLIBCXX_3.4.16
GLIBCXX_3.4.17
GLIBCXX_3.4.18
GLIBCXX_3.4.19
GLIBCXX_3.4.20
GLIBCXX_3.4.21
GLIBCXX_3.4.22
GLIBCXX_3.4.23
GLIBCXX_3.4.24
GLIBCXX_3.4.25
GLIBCXX_DEBUG_MESSAGE_LENGTH
Mario Sergio Valdes
Mar 11, 2022, 1:52:27 AM3/11/22
to gmx_MMPBSA
And the rest? Because if it works for ubuntu 16.04 it should work for 18.04. Interestingly, we tested it and gmx_MMPBSA worked fine on Ubuntu 18.04
Ketan Rohilla
Mar 11, 2022, 1:58:54 AM3/11/22
to gmx_MMPBSA
[sudo] password for manoj:
Toolchain test builds; see https://wiki.ubuntu.com/ToolChain
More info: https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test
Press [ENTER] to continue or Ctrl-c to cancel adding it.
Hit:1 http://in.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://in.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://in.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 http://ppa.launchpad.net/otto-kesselgulasch/gimp/ubuntu bionic InRelease
Get:5 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]
Hit:6 http://deb.anydesk.com all InRelease
Hit:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu bionic InRelease
Err:6 http://deb.anydesk.com all InRelease
The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
Get:8 http://security.ubuntu.com/ubuntu bionic-security/main amd64 DEP-11 Metadata [55.1 kB]
Get:9 http://security.ubuntu.com/ubuntu bionic-security/universe amd64 DEP-11 Metadata [59.4 kB]
Get:10 http://security.ubuntu.com/ubuntu bionic-security/multiverse amd64 DEP-11 Metadata [2,464 B]
Fetched 206 kB in 2s (94.9 kB/s)
Reading package lists... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://deb.anydesk.com all InRelease: The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Failed to fetch http://deb.anydesk.com/dists/all/InRelease The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Some index files failed to download. They have been ignored, or old ones used instead.
(gmxMMPBSA) manoj@manoj:~$ sudo apt update
Hit:1 http://in.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://in.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://in.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 http://deb.anydesk.com all InRelease
Hit:5 http://ppa.launchpad.net/otto-kesselgulasch/gimp/ubuntu bionic InRelease
Hit:6 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu bionic InRelease
Err:4 http://deb.anydesk.com all InRelease
The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
Reading package lists... Done
Building dependency tree
Reading state information... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://deb.anydesk.com all InRelease: The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Failed to fetch http://deb.anydesk.com/dists/all/InRelease The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Some index files failed to download. They have been ignored, or old ones used instead.
(gmxMMPBSA) manoj@manoj:~$ sudo apt install gcc-4.9
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package gcc-4.9 is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
E: Package 'gcc-4.9' has no installation candidate
Reading package lists... Done
Building dependency tree
Reading state information... Done
Mario Sergio Valdes
Mar 11, 2022, 2:33:23 AM3/11/22
to gmx_MMPBSA
Follow these instructions:
sudo apt install upgrade libstdc++6
Check the supported versions again
Check the supported versions
strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
Add this repo and update the libstdc++6 library
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt update
sudo apt update
sudo apt install gcc-5 or sudo apt install gcc-6 (For me works with the version 5)
sudo apt install upgrade libstdc++6
Check the supported versions again
strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBCXX
The version must be >= 3.4.29
Ketan Rohilla
Mar 11, 2022, 4:45:28 AM3/11/22
to gmx_MMPBSA
Still not working with gcc-5 or gcc-6.
Hit:6 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu bionic InRelease
Err:5 http://deb.anydesk.com all InRelease Hit:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu bionic InRelease
The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
Reading package lists... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://deb.anydesk.com all InRelease: The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Failed to fetch http://deb.anydesk.com/dists/all/InRelease The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Some index files failed to download. They have been ignored, or old ones used instead.
(gmxMMPBSA) manoj@manoj:~$ sudo apt update
Hit:1 http://in.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://in.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://in.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 http://deb.anydesk.com all InRelease
Hit:5 http://ppa.launchpad.net/otto-kesselgulasch/gimp/ubuntu bionic InRelease
Hit:6 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu bionic InRelease
Err:4 http://deb.anydesk.com all InRelease
The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
Reading package lists... Done
Building dependency tree
Reading state information... Done
21 packages can be upgraded. Run 'apt list --upgradable' to see them.
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://deb.anydesk.com all InRelease: The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Failed to fetch http://deb.anydesk.com/dists/all/InRelease The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Some index files failed to download. They have been ignored, or old ones used instead.
(gmxMMPBSA) manoj@manoj:~$ sudo apt install gcc-6Reading package lists... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://deb.anydesk.com all InRelease: The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Failed to fetch http://deb.anydesk.com/dists/all/InRelease The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Some index files failed to download. They have been ignored, or old ones used instead.
(gmxMMPBSA) manoj@manoj:~$ sudo apt update
Hit:1 http://in.archive.ubuntu.com/ubuntu bionic InRelease
Hit:2 http://in.archive.ubuntu.com/ubuntu bionic-updates InRelease
Hit:3 http://in.archive.ubuntu.com/ubuntu bionic-backports InRelease
Hit:4 http://deb.anydesk.com all InRelease
Hit:5 http://ppa.launchpad.net/otto-kesselgulasch/gimp/ubuntu bionic InRelease
Hit:6 http://security.ubuntu.com/ubuntu bionic-security InRelease
Hit:7 http://ppa.launchpad.net/ubuntu-toolchain-r/test/ubuntu bionic InRelease
Err:4 http://deb.anydesk.com all InRelease
The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
Reading package lists... Done
Building dependency tree
Reading state information... Done
21 packages can be upgraded. Run 'apt list --upgradable' to see them.
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://deb.anydesk.com all InRelease: The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Failed to fetch http://deb.anydesk.com/dists/all/InRelease The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Some index files failed to download. They have been ignored, or old ones used instead.
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
gir1.2-geocodeglib-1.0 libfwup1 libllvm7 libllvm8 libllvm9 shim
ubuntu-web-launchers
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 21 not upgraded.
(gmxMMPBSA) manoj@manoj:~$ sudo apt install upgrade libstdc++6
Reading package lists... Done
Building dependency tree
Reading state information... Done
E: Unable to locate package upgrade
Mario Sergio Valdes
Mar 11, 2022, 12:52:43 PM3/11/22
to gmx_MMPBSA
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used.
Here is your problem. A repository has problems so a new index is not generated. Delete this repository, and do the procedure I indicated again
Ketan Rohilla
Mar 12, 2022, 3:45:00 AM3/12/22
to gmx_MMPBSA
Which repository do I need to delete?
GNU nano 2.9.3 /etc/apt/sources.list
# deb cdrom:[Ubuntu 16.04.4 LTS _Xenial Xerus_ - Release amd64 (20180228)]/ xenial main restricted
# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://in.archive.ubuntu.com/ubuntu/ bionic main restricted
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial main restricted
## Major bug fix updates produced after the final release of the
## distribution.
deb http://in.archive.ubuntu.com/ubuntu/ bionic-updates main restricted
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial-updates main restricted
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://in.archive.ubuntu.com/ubuntu/ bionic universe
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial universe
deb http://in.archive.ubuntu.com/ubuntu/ bionic-updates universe
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial-updates universe
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://in.archive.ubuntu.com/ubuntu/ bionic multiverse
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial multiverse
deb http://in.archive.ubuntu.com/ubuntu/ bionic-updates multiverse
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial-updates multiverse
## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://in.archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse
## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb http://archive.canonical.com/ubuntu xenial partner
# deb-src http://archive.canonical.com/ubuntu xenial partner
deb http://security.ubuntu.com/ubuntu bionic-security main restricted
# deb-src http://security.ubuntu.com/ubuntu xenial-security main restricted
deb http://security.ubuntu.com/ubuntu bionic-security universe
# deb-src http://security.ubuntu.com/ubuntu xenial-security universe
deb http://security.ubuntu.com/ubuntu bionic-security multiverse
# deb-src http://security.ubuntu.com/ubuntu xenial-security multiverse
# deb http://www.openprinting.org/download/printdriver/debian/ lsb3.2 contrib # disabled on upgrade to bionic
# deb cdrom:[Ubuntu 16.04.4 LTS _Xenial Xerus_ - Release amd64 (20180228)]/ xenial main restricted
# See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
# newer versions of the distribution.
deb http://in.archive.ubuntu.com/ubuntu/ bionic main restricted
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial main restricted
## Major bug fix updates produced after the final release of the
## distribution.
deb http://in.archive.ubuntu.com/ubuntu/ bionic-updates main restricted
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial-updates main restricted
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team. Also, please note that software in universe WILL NOT receive any
## review or updates from the Ubuntu security team.
deb http://in.archive.ubuntu.com/ubuntu/ bionic universe
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial universe
deb http://in.archive.ubuntu.com/ubuntu/ bionic-updates universe
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial-updates universe
## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
## team, and may not be under a free licence. Please satisfy yourself as to
## your rights to use the software. Also, please note that software in
## multiverse WILL NOT receive any review or updates from the Ubuntu
## security team.
deb http://in.archive.ubuntu.com/ubuntu/ bionic multiverse
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial multiverse
deb http://in.archive.ubuntu.com/ubuntu/ bionic-updates multiverse
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial-updates multiverse
## N.B. software from this repository may not have been tested as
## extensively as that contained in the main release, although it includes
## newer versions of some applications which may provide useful features.
## Also, please note that software in backports WILL NOT receive any review
## or updates from the Ubuntu security team.
deb http://in.archive.ubuntu.com/ubuntu/ bionic-backports main restricted universe multiverse
# deb-src http://in.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse
## Uncomment the following two lines to add software from Canonical's
## 'partner' repository.
## This software is not part of Ubuntu, but is offered by Canonical and the
## respective vendors as a service to Ubuntu users.
# deb http://archive.canonical.com/ubuntu xenial partner
# deb-src http://archive.canonical.com/ubuntu xenial partner
deb http://security.ubuntu.com/ubuntu bionic-security main restricted
# deb-src http://security.ubuntu.com/ubuntu xenial-security main restricted
deb http://security.ubuntu.com/ubuntu bionic-security universe
# deb-src http://security.ubuntu.com/ubuntu xenial-security universe
deb http://security.ubuntu.com/ubuntu bionic-security multiverse
# deb-src http://security.ubuntu.com/ubuntu xenial-security multiverse
# deb http://www.openprinting.org/download/printdriver/debian/ lsb3.2 contrib # disabled on upgrade to bionic
Mario Sergio Valdes
Mar 12, 2022, 11:17:49 AM3/12/22
to gmx_MMPBSA
This
Err:5 http://deb.anydesk.com all InRelease
The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
Reading package lists... Done
W: An error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://deb.anydesk.com all InRelease: The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Failed to fetch http://deb.anydesk.com/dists/all/InRelease The following signatures were invalid: EXPKEYSIG 18DF3741CDFFDE29 philandro Software GmbH <in...@philandro.com>
W: Some index files failed to download. They have been ignored, or old ones used instead.
Probably you can find it in Softwares & Updates manager. Install both gcc-5 and gcc-6
Ketan Rohilla
Mar 14, 2022, 1:30:11 AM3/14/22
to gmx_MMPBSA
Its working on UBUNTU now. Thanks!
One thing I want to ask about running on HPC user account. I have installed gmx_MMPBSA in root account. It is working when I login as root. But when I login as admin account. It says command not found, Please help!
[admin@nmrmkp ~]$ conda info --envs
# conda environments:
#
base * /home/admin/anaconda3
gmxMMPBSA /home/admin/anaconda3/envs/gmxMMPBSA
mdaenv /home/admin/anaconda3/envs/mdaenv
nmr /home/admin/anaconda3/envs/nmr
[admin@nmrmkp ~]$ conda activate gmxMMPBSA
(gmxMMPBSA) [admin@nmrmkp ~]$ gmx_MMPBSA
bash: gmx_MMPBSA: command not found...
(gmxMMPBSA) [admin@nmrmkp ~]$
# conda environments:
#
base * /home/admin/anaconda3
gmxMMPBSA /home/admin/anaconda3/envs/gmxMMPBSA
mdaenv /home/admin/anaconda3/envs/mdaenv
nmr /home/admin/anaconda3/envs/nmr
[admin@nmrmkp ~]$ conda activate gmxMMPBSA
(gmxMMPBSA) [admin@nmrmkp ~]$ gmx_MMPBSA
bash: gmx_MMPBSA: command not found...
(gmxMMPBSA) [admin@nmrmkp ~]$
Mario Sergio Valdes
Mar 14, 2022, 1:59:07 AM3/14/22
to gmx_MMPBSA
It is not a good practice to install programs as root due to several factors, among them, security issues and the accessibility of other users. In the first case, you have no problems, because we assure you that gmx_MMPBSA is completely safe. However, the second aspect is easier to solve by installing gmx_MMPBSA locally on your user, since it is a conda environment. Here are some links where you can find details of such installation
HTH!
Mario S.
Ketan Rohilla
Mar 14, 2022, 2:13:21 AM3/14/22
to gmx_MMPBSA
I will look upon your suggestions, Thanks! gmx_MMPBSA_ana is showing the following error in Centos7 now:
Traceback (most recent call last):
File "/root/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA_ana", line 8, in <module>
sys.exit(gmxmmpbsa_ana())
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 131, in gmxmmpbsa_ana
from GMXMMPBSA.analyzer.gui import GMX_MMPBSA_ANA
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/analyzer/gui.py", line 33, in <module>
import pandas as pd
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/__init__.py", line 48, in <module>
from pandas.core.api import (
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/api.py", line 48, in <module>
from pandas.core.groupby import (
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/groupby/__init__.py", line 1, in <module>
from pandas.core.groupby.generic import (
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/groupby/generic.py", line 70, in <module>
from pandas.core.frame import DataFrame
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/frame.py", line 157, in <module>
from pandas.core.generic import NDFrame
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/generic.py", line 152, in <module>
from pandas.core.window import (
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/window/__init__.py", line 1, in <module>
from pandas.core.window.ewm import ( # noqa:F401
File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/core/window/ewm.py", line 12, in <module>
import pandas._libs.window.aggregations as window_aggregations
ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found (required by /root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/pandas/_libs/window/aggregations.cpython-39-x86_64-linux-gnu.so)
Mario Sergio Valdes
Mar 14, 2022, 2:21:29 AM3/14/22
to gmx_MMPBSA
This is the same error as the previous one. In this case, pandas search the GLIBCXX_3.4.21 library in /lib64 instead of /usr/lib. To fix it, make a symbolic link in that address.
Note that Centos 7 is an outdated operating system and server-dedicated. It may or may not work. In the link, I sent you they explain why HPCs are not ideal for GUI. To analyze the results, copy the working folder to your PC with a newer OS and run gmx_MMPBSA_ana as described in the documentation (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/gmx_MMPBSA_ana_running/#running-gmx_mmpbsa_ana)
Note that Centos 7 is an outdated operating system and server-dedicated. It may or may not work. In the link, I sent you they explain why HPCs are not ideal for GUI. To analyze the results, copy the working folder to your PC with a newer OS and run gmx_MMPBSA_ana as described in the documentation (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/gmx_MMPBSA_ana_running/#running-gmx_mmpbsa_ana)
Ketan Rohilla
Mar 14, 2022, 2:30:13 AM3/14/22
to gmx_MMPBSA
Can gmx_MMPBSA_ana be installed on windows operating system also?
Mario Sergio Valdes
Mar 14, 2022, 2:41:33 AM3/14/22
to gmx_MMPBSA
No, only Linux and macOS
Ketan Rohilla
Mar 15, 2022, 12:26:23 AM3/15/22
to gmx_MMPBSA
Is there any other way to analyze results in case gmx_MMPBSA_ana doesn't work?
Mario Sergio Valdes
Mar 15, 2022, 12:31:18 AM3/15/22
to gmx_MMPBSA
Yes, you can save the data in csv format using -eo and -deo options. Please check the documentation (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/gmx_MMPBSA_command-line/). If you already run the calculations, you can rewrite the output using these options, examples gmx_MMPBSA -rewrite-output -deo and/or -eo
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