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Navneet Kumar
Apr 16, 2022, 12:56:07 PM4/16/22
to gmx_MMPBSA
Hi! Please help me with the installation.
Please find the full report of installation.
glab-5000@pglab6000-lenovo-p520:~$ conda create -n gmxMMPBSA python=3.9 -y -qCollecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/pglab-5000/miniconda3/envs/gmxMMPBSA
added / updated specs:
- python=3.9
The following packages will be downloaded:
package | build
---------------------------|-----------------
ca-certificates-2022.3.29 | h06a4308_0 117 KB
python-3.9.12 | h12debd9_0 19.1 MB
setuptools-61.2.0 | py39h06a4308_0 1011 KB
sqlite-3.38.2 | hc218d9a_0 1.0 MB
tzdata-2022a | hda174b7_0 109 KB
------------------------------------------------------------
Total: 21.4 MB
The following NEW packages will be INSTALLED:
_libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main
_openmp_mutex pkgs/main/linux-64::_openmp_mutex-4.5-1_gnu
ca-certificates pkgs/main/linux-64::ca-certificates-2022.3.29-h06a4308_0
certifi pkgs/main/linux-64::certifi-2021.10.8-py39h06a4308_2
ld_impl_linux-64 pkgs/main/linux-64::ld_impl_linux-64-2.35.1-h7274673_9
libffi pkgs/main/linux-64::libffi-3.3-he6710b0_2
libgcc-ng pkgs/main/linux-64::libgcc-ng-9.3.0-h5101ec6_17
libgomp pkgs/main/linux-64::libgomp-9.3.0-h5101ec6_17
libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.3.0-hd4cf53a_17
ncurses pkgs/main/linux-64::ncurses-6.3-h7f8727e_2
openssl pkgs/main/linux-64::openssl-1.1.1n-h7f8727e_0
pip pkgs/main/linux-64::pip-21.2.4-py39h06a4308_0
python pkgs/main/linux-64::python-3.9.12-h12debd9_0
readline pkgs/main/linux-64::readline-8.1.2-h7f8727e_1
setuptools pkgs/main/linux-64::setuptools-61.2.0-py39h06a4308_0
sqlite pkgs/main/linux-64::sqlite-3.38.2-hc218d9a_0
tk pkgs/main/linux-64::tk-8.6.11-h1ccaba5_0
tzdata pkgs/main/noarch::tzdata-2022a-hda174b7_0
wheel pkgs/main/noarch::wheel-0.37.1-pyhd3eb1b0_0
xz pkgs/main/linux-64::xz-5.2.5-h7b6447c_0
zlib pkgs/main/linux-64::zlib-1.2.11-h7f8727e_4
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
pglab-5000@pglab6000-lenovo-p520:~$ conda activate gmxMMPBSA
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
## Package Plan ##
environment location: /home/pglab-5000/miniconda3/envs/gmxMMPBSA
added / updated specs:
- ambertools=21.12
- compilers
- mpi4py=3.1.3
The following packages will be downloaded:
package | build
---------------------------|-----------------
_libgcc_mutex-0.1 | conda_forge 3 KB conda-forge
_openmp_mutex-4.5 | 1_gnu 22 KB conda-forge
ambertools-21.12 | py39hc630cb1_0 89.2 MB conda-forge
arpack-3.7.0 | hdefa2d7_2 215 KB conda-forge
binutils-2.35.1 | hdd6e379_2 26 KB conda-forge
binutils_impl_linux-64-2.35.1| h27ae35d_9 3.6 MB
binutils_linux-64-2.35 | h67ddf6f_30 22 KB conda-forge
boost-cpp-1.74.0 | h75c5d50_8 16.2 MB conda-forge
brotli-1.0.9 | h166bdaf_7 18 KB conda-forge
brotli-bin-1.0.9 | h166bdaf_7 19 KB conda-forge
bzip2-1.0.8 | h7f98852_4 484 KB conda-forge
c-ares-1.18.1 | h7f98852_0 113 KB conda-forge
c-compiler-1.2.0 | h7f98852_0 6 KB conda-forge
ca-certificates-2021.10.8 | ha878542_0 139 KB conda-forge
certifi-2021.10.8 | py39hf3d152e_2 145 KB conda-forge
compilers-1.2.0 | ha770c72_0 5 KB conda-forge
curl-7.82.0 | h7bff187_0 90 KB conda-forge
cxx-compiler-1.2.0 | h4bd325d_0 6 KB conda-forge
cycler-0.11.0 | pyhd8ed1ab_0 10 KB conda-forge
cython-0.29.28 | py39h5a03fae_2 2.1 MB conda-forge
fftw-3.3.10 |nompi_h77c792f_102 6.4 MB conda-forge
fonttools-4.32.0 | py39hb9d737c_0 1.6 MB conda-forge
fortran-compiler-1.2.0 | h1990efc_0 6 KB conda-forge
freetype-2.10.4 | h0708190_1 890 KB conda-forge
fribidi-1.0.10 | h36c2ea0_0 112 KB conda-forge
gcc_impl_linux-64-9.3.0 | h6df7d76_17 44.6 MB
gcc_linux-64-9.3.0 | hf25ea35_30 23 KB conda-forge
gfortran_impl_linux-64-9.3.0| hc4a2995_19 10.1 MB conda-forge
gfortran_linux-64-9.3.0 | hdc58fab_30 22 KB conda-forge
giflib-5.2.1 | h36c2ea0_2 77 KB conda-forge
gxx_impl_linux-64-9.3.0 | hbdd7822_17 9.0 MB
gxx_linux-64-9.3.0 | h3fbe746_30 23 KB conda-forge
hdf4-4.2.15 | h10796ff_3 950 KB conda-forge
hdf5-1.12.1 |nompi_h2750804_103 3.6 MB conda-forge
icu-70.1 | h27087fc_0 13.5 MB conda-forge
jbig-2.1 | h7f98852_2003 43 KB conda-forge
jpeg-9e | h7f98852_0 269 KB conda-forge
kernel-headers_linux-64-2.6.32| he073ed8_15 707 KB conda-forge
keyutils-1.6.1 | h166bdaf_0 115 KB conda-forge
kiwisolver-1.4.2 | py39hf939315_1 75 KB conda-forge
krb5-1.19.3 | h3790be6_0 1.4 MB conda-forge
lcms2-2.12 | hddcbb42_0 443 KB conda-forge
lerc-3.0 | h9c3ff4c_0 216 KB conda-forge
libblas-3.9.0 |13_linux64_openblas 12 KB conda-forge
libbrotlicommon-1.0.9 | h166bdaf_7 65 KB conda-forge
libbrotlidec-1.0.9 | h166bdaf_7 33 KB conda-forge
libbrotlienc-1.0.9 | h166bdaf_7 287 KB conda-forge
libcblas-3.9.0 |13_linux64_openblas 12 KB conda-forge
libcurl-7.82.0 | h7bff187_0 341 KB conda-forge
libdeflate-1.10 | h7f98852_0 77 KB conda-forge
libedit-3.1.20191231 | he28a2e2_2 121 KB conda-forge
libev-4.33 | h516909a_1 104 KB conda-forge
libgcc-devel_linux-64-9.3.0| hb95220a_17 2.8 MB
libgcc-ng-11.2.0 | h1d223b6_15 911 KB conda-forge
libgfortran-ng-9.4.0 | h69a702a_15 23 KB conda-forge
libgfortran5-9.4.0 | h62347ff_15 1.9 MB conda-forge
libgomp-11.2.0 | h1d223b6_15 432 KB conda-forge
libimagequant-2.17.0 | h7f98852_1 48 KB conda-forge
liblapack-3.9.0 |13_linux64_openblas 12 KB conda-forge
libnetcdf-4.8.1 |nompi_hb3fd0d9_101 1.5 MB conda-forge
libnghttp2-1.47.0 | h727a467_0 808 KB conda-forge
libnsl-2.0.0 | h7f98852_0 31 KB conda-forge
libopenblas-0.3.18 |pthreads_h8fe5266_0 9.6 MB conda-forge
libpng-1.6.37 | h21135ba_2 306 KB conda-forge
libssh2-1.10.0 | ha56f1ee_2 233 KB conda-forge
libstdcxx-devel_linux-64-9.3.0| hf0c5c8d_17 10.6 MB
libstdcxx-ng-11.2.0 | he4da1e4_15 4.2 MB conda-forge
libtiff-4.3.0 | h542a066_3 638 KB conda-forge
libuuid-2.32.1 | h7f98852_1000 28 KB conda-forge
libwebp-1.2.2 | h3452ae3_0 85 KB conda-forge
libwebp-base-1.2.2 | h7f98852_1 824 KB conda-forge
libxcb-1.13 | h7f98852_1004 391 KB conda-forge
libzip-1.8.0 | h4de3113_1 126 KB conda-forge
libzlib-1.2.11 | h166bdaf_1014 60 KB conda-forge
lz4-c-1.9.3 | h9c3ff4c_1 179 KB conda-forge
matplotlib-base-3.5.1 | py39h2fa2bec_0 7.4 MB conda-forge
mpi-1.0 | openmpi 4 KB conda-forge
mpi4py-3.1.3 | py39hc649577_0 665 KB conda-forge
munkres-1.1.4 | pyh9f0ad1d_0 12 KB conda-forge
netcdf-fortran-4.5.4 |nompi_h2b6e579_100 1.3 MB conda-forge
numpy-1.22.3 | py39h18676bf_2 6.8 MB conda-forge
openjpeg-2.4.0 | hb52868f_1 444 KB conda-forge
openmpi-4.1.2 | hbfc84c5_0 4.3 MB conda-forge
openssl-1.1.1n | h166bdaf_0 2.1 MB conda-forge
packaging-21.3 | pyhd8ed1ab_0 36 KB conda-forge
packmol-20.010 | h86c2bf4_0 129 KB conda-forge
pandas-1.4.2 | py39h1832856_1 12.5 MB conda-forge
parmed-3.4.3 | py39h5a03fae_2 972 KB conda-forge
perl-5.32.1 | 2_h7f98852_perl5 14.4 MB conda-forge
pillow-9.0.1 | py39he69867a_1 44.5 MB conda-forge
pthread-stubs-0.4 | h36c2ea0_1001 5 KB conda-forge
pyparsing-3.0.8 | pyhd8ed1ab_0 79 KB conda-forge
python-dateutil-2.8.2 | pyhd8ed1ab_0 240 KB conda-forge
python_abi-3.9 | 2_cp39 4 KB conda-forge
pytz-2022.1 | pyhd8ed1ab_0 242 KB conda-forge
scipy-1.8.0 | py39hee8e79c_1 25.4 MB conda-forge
six-1.16.0 | pyh6c4a22f_0 14 KB conda-forge
sysroot_linux-64-2.12 | he073ed8_15 31.4 MB conda-forge
unicodedata2-14.0.0 | py39hb9d737c_1 498 KB conda-forge
xorg-kbproto-1.0.7 | h7f98852_1002 27 KB conda-forge
xorg-libice-1.0.10 | h7f98852_0 58 KB conda-forge
xorg-libsm-1.2.3 | hd9c2040_1000 26 KB conda-forge
xorg-libx11-1.7.2 | h7f98852_0 941 KB conda-forge
xorg-libxau-1.0.9 | h7f98852_0 13 KB conda-forge
xorg-libxdmcp-1.1.3 | h7f98852_0 19 KB conda-forge
xorg-libxext-1.3.4 | h7f98852_1 54 KB conda-forge
xorg-libxt-1.2.1 | h7f98852_2 375 KB conda-forge
xorg-xextproto-7.3.0 | h7f98852_1002 28 KB conda-forge
xorg-xproto-7.0.31 | h7f98852_1007 73 KB conda-forge
zlib-1.2.11 | h166bdaf_1014 88 KB conda-forge
zstd-1.5.2 | ha95c52a_0 458 KB conda-forge
------------------------------------------------------------
Total: 398.6 MB
The following NEW packages will be INSTALLED:
ambertools conda-forge/linux-64::ambertools-21.12-py39hc630cb1_0
arpack conda-forge/linux-64::arpack-3.7.0-hdefa2d7_2
binutils conda-forge/linux-64::binutils-2.35.1-hdd6e379_2
binutils_impl_lin~ pkgs/main/linux-64::binutils_impl_linux-64-2.35.1-h27ae35d_9
binutils_linux-64 conda-forge/linux-64::binutils_linux-64-2.35-h67ddf6f_30
boost-cpp conda-forge/linux-64::boost-cpp-1.74.0-h75c5d50_8
brotli conda-forge/linux-64::brotli-1.0.9-h166bdaf_7
brotli-bin conda-forge/linux-64::brotli-bin-1.0.9-h166bdaf_7
bzip2 conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
c-ares conda-forge/linux-64::c-ares-1.18.1-h7f98852_0
c-compiler conda-forge/linux-64::c-compiler-1.2.0-h7f98852_0
compilers conda-forge/linux-64::compilers-1.2.0-ha770c72_0
curl conda-forge/linux-64::curl-7.82.0-h7bff187_0
cxx-compiler conda-forge/linux-64::cxx-compiler-1.2.0-h4bd325d_0
cycler conda-forge/noarch::cycler-0.11.0-pyhd8ed1ab_0
cython conda-forge/linux-64::cython-0.29.28-py39h5a03fae_2
fftw conda-forge/linux-64::fftw-3.3.10-nompi_h77c792f_102
fonttools conda-forge/linux-64::fonttools-4.32.0-py39hb9d737c_0
fortran-compiler conda-forge/linux-64::fortran-compiler-1.2.0-h1990efc_0
freetype conda-forge/linux-64::freetype-2.10.4-h0708190_1
fribidi conda-forge/linux-64::fribidi-1.0.10-h36c2ea0_0
gcc_impl_linux-64 pkgs/main/linux-64::gcc_impl_linux-64-9.3.0-h6df7d76_17
gcc_linux-64 conda-forge/linux-64::gcc_linux-64-9.3.0-hf25ea35_30
gfortran_impl_lin~ conda-forge/linux-64::gfortran_impl_linux-64-9.3.0-hc4a2995_19
gfortran_linux-64 conda-forge/linux-64::gfortran_linux-64-9.3.0-hdc58fab_30
giflib conda-forge/linux-64::giflib-5.2.1-h36c2ea0_2
gxx_impl_linux-64 pkgs/main/linux-64::gxx_impl_linux-64-9.3.0-hbdd7822_17
gxx_linux-64 conda-forge/linux-64::gxx_linux-64-9.3.0-h3fbe746_30
hdf4 conda-forge/linux-64::hdf4-4.2.15-h10796ff_3
hdf5 conda-forge/linux-64::hdf5-1.12.1-nompi_h2750804_103
icu conda-forge/linux-64::icu-70.1-h27087fc_0
jbig conda-forge/linux-64::jbig-2.1-h7f98852_2003
jpeg conda-forge/linux-64::jpeg-9e-h7f98852_0
kernel-headers_li~ conda-forge/noarch::kernel-headers_linux-64-2.6.32-he073ed8_15
keyutils conda-forge/linux-64::keyutils-1.6.1-h166bdaf_0
kiwisolver conda-forge/linux-64::kiwisolver-1.4.2-py39hf939315_1
krb5 conda-forge/linux-64::krb5-1.19.3-h3790be6_0
lcms2 conda-forge/linux-64::lcms2-2.12-hddcbb42_0
lerc conda-forge/linux-64::lerc-3.0-h9c3ff4c_0
libblas conda-forge/linux-64::libblas-3.9.0-13_linux64_openblas
libbrotlicommon conda-forge/linux-64::libbrotlicommon-1.0.9-h166bdaf_7
libbrotlidec conda-forge/linux-64::libbrotlidec-1.0.9-h166bdaf_7
libbrotlienc conda-forge/linux-64::libbrotlienc-1.0.9-h166bdaf_7
libcblas conda-forge/linux-64::libcblas-3.9.0-13_linux64_openblas
libcurl conda-forge/linux-64::libcurl-7.82.0-h7bff187_0
libdeflate conda-forge/linux-64::libdeflate-1.10-h7f98852_0
libedit conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
libev conda-forge/linux-64::libev-4.33-h516909a_1
libgcc-devel_linu~ pkgs/main/linux-64::libgcc-devel_linux-64-9.3.0-hb95220a_17
libgfortran-ng conda-forge/linux-64::libgfortran-ng-9.4.0-h69a702a_15
libgfortran5 conda-forge/linux-64::libgfortran5-9.4.0-h62347ff_15
libimagequant conda-forge/linux-64::libimagequant-2.17.0-h7f98852_1
liblapack conda-forge/linux-64::liblapack-3.9.0-13_linux64_openblas
libnetcdf conda-forge/linux-64::libnetcdf-4.8.1-nompi_hb3fd0d9_101
libnghttp2 conda-forge/linux-64::libnghttp2-1.47.0-h727a467_0
libnsl conda-forge/linux-64::libnsl-2.0.0-h7f98852_0
libopenblas conda-forge/linux-64::libopenblas-0.3.18-pthreads_h8fe5266_0
libpng conda-forge/linux-64::libpng-1.6.37-h21135ba_2
libssh2 conda-forge/linux-64::libssh2-1.10.0-ha56f1ee_2
libstdcxx-devel_l~ pkgs/main/linux-64::libstdcxx-devel_linux-64-9.3.0-hf0c5c8d_17
libtiff conda-forge/linux-64::libtiff-4.3.0-h542a066_3
libuuid conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000
libwebp conda-forge/linux-64::libwebp-1.2.2-h3452ae3_0
libwebp-base conda-forge/linux-64::libwebp-base-1.2.2-h7f98852_1
libxcb conda-forge/linux-64::libxcb-1.13-h7f98852_1004
libzip conda-forge/linux-64::libzip-1.8.0-h4de3113_1
libzlib conda-forge/linux-64::libzlib-1.2.11-h166bdaf_1014
lz4-c conda-forge/linux-64::lz4-c-1.9.3-h9c3ff4c_1
matplotlib-base conda-forge/linux-64::matplotlib-base-3.5.1-py39h2fa2bec_0
mpi conda-forge/linux-64::mpi-1.0-openmpi
mpi4py conda-forge/linux-64::mpi4py-3.1.3-py39hc649577_0
munkres conda-forge/noarch::munkres-1.1.4-pyh9f0ad1d_0
netcdf-fortran conda-forge/linux-64::netcdf-fortran-4.5.4-nompi_h2b6e579_100
numpy conda-forge/linux-64::numpy-1.22.3-py39h18676bf_2
openjpeg conda-forge/linux-64::openjpeg-2.4.0-hb52868f_1
openmpi conda-forge/linux-64::openmpi-4.1.2-hbfc84c5_0
packaging conda-forge/noarch::packaging-21.3-pyhd8ed1ab_0
packmol conda-forge/linux-64::packmol-20.010-h86c2bf4_0
pandas conda-forge/linux-64::pandas-1.4.2-py39h1832856_1
parmed conda-forge/linux-64::parmed-3.4.3-py39h5a03fae_2
perl conda-forge/linux-64::perl-5.32.1-2_h7f98852_perl5
pillow conda-forge/linux-64::pillow-9.0.1-py39he69867a_1
pthread-stubs conda-forge/linux-64::pthread-stubs-0.4-h36c2ea0_1001
pyparsing conda-forge/noarch::pyparsing-3.0.8-pyhd8ed1ab_0
python-dateutil conda-forge/noarch::python-dateutil-2.8.2-pyhd8ed1ab_0
python_abi conda-forge/linux-64::python_abi-3.9-2_cp39
pytz conda-forge/noarch::pytz-2022.1-pyhd8ed1ab_0
scipy conda-forge/linux-64::scipy-1.8.0-py39hee8e79c_1
six conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
sysroot_linux-64 conda-forge/noarch::sysroot_linux-64-2.12-he073ed8_15
unicodedata2 conda-forge/linux-64::unicodedata2-14.0.0-py39hb9d737c_1
xorg-kbproto conda-forge/linux-64::xorg-kbproto-1.0.7-h7f98852_1002
xorg-libice conda-forge/linux-64::xorg-libice-1.0.10-h7f98852_0
xorg-libsm conda-forge/linux-64::xorg-libsm-1.2.3-hd9c2040_1000
xorg-libx11 conda-forge/linux-64::xorg-libx11-1.7.2-h7f98852_0
xorg-libxau conda-forge/linux-64::xorg-libxau-1.0.9-h7f98852_0
xorg-libxdmcp conda-forge/linux-64::xorg-libxdmcp-1.1.3-h7f98852_0
xorg-libxext conda-forge/linux-64::xorg-libxext-1.3.4-h7f98852_1
xorg-libxt conda-forge/linux-64::xorg-libxt-1.2.1-h7f98852_2
xorg-xextproto conda-forge/linux-64::xorg-xextproto-7.3.0-h7f98852_1002
xorg-xproto conda-forge/linux-64::xorg-xproto-7.0.31-h7f98852_1007
zstd conda-forge/linux-64::zstd-1.5.2-ha95c52a_0
The following packages will be UPDATED:
libgcc-ng pkgs/main::libgcc-ng-9.3.0-h5101ec6_17 --> conda-forge::libgcc-ng-11.2.0-h1d223b6_15
libgomp pkgs/main::libgomp-9.3.0-h5101ec6_17 --> conda-forge::libgomp-11.2.0-h1d223b6_15
libstdcxx-ng pkgs/main::libstdcxx-ng-9.3.0-hd4cf53~ --> conda-forge::libstdcxx-ng-11.2.0-he4da1e4_15
zlib pkgs/main::zlib-1.2.11-h7f8727e_4 --> conda-forge::zlib-1.2.11-h166bdaf_1014
The following packages will be SUPERSEDED by a higher-priority channel:
_libgcc_mutex pkgs/main::_libgcc_mutex-0.1-main --> conda-forge::_libgcc_mutex-0.1-conda_forge
_openmp_mutex pkgs/main --> conda-forge
ca-certificates pkgs/main::ca-certificates-2022.3.29-~ --> conda-forge::ca-certificates-2021.10.8-ha878542_0
certifi pkgs/main::certifi-2021.10.8-py39h06a~ --> conda-forge::certifi-2021.10.8-py39hf3d152e_2
openssl pkgs/main::openssl-1.1.1n-h7f8727e_0 --> conda-forge::openssl-1.1.1n-h166bdaf_0
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working...
For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by default.
To enable it, please set the environment variable OMPI_MCA_opal_cuda_support=true before
launching your MPI processes. Equivalently, you can set the MCA parameter in the command line:
mpiexec --mca opal_cuda_support 1 ...
In addition, the UCX support is also built but disabled by default.
To enable it, first install UCX (conda install -c conda-forge ucx). Then, set the environment
variables OMPI_MCA_pml="ucx" OMPI_MCA_osc="ucx" before launching your MPI processes.
Equivalently, you can set the MCA parameters in the command line:
mpiexec --mca pml ucx --mca osc ucx ...
Note that you might also need to set UCX_MEMTYPE_CACHE=n for CUDA awareness via UCX.
Please consult UCX's documentation for detail.
done
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ python -m pip install pyqt5
Collecting pyqt5
Downloading PyQt5-5.15.6-cp36-abi3-manylinux1_x86_64.whl (8.3 MB)
|████████████████████████████████| 8.3 MB 80 kB/s
Collecting PyQt5-sip<13,>=12.8
Downloading PyQt5_sip-12.10.1-cp39-cp39-manylinux1_x86_64.whl (349 kB)
|████████████████████████████████| 349 kB 4.1 MB/s
Collecting PyQt5-Qt5>=5.15.2
Downloading PyQt5_Qt5-5.15.2-py3-none-manylinux2014_x86_64.whl (59.9 MB)
|████████████████████████████████| 59.9 MB 168 kB/s
Installing collected packages: PyQt5-sip, PyQt5-Qt5, pyqt5
Successfully installed PyQt5-Qt5-5.15.2 PyQt5-sip-12.10.1 pyqt5-5.15.6
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ gmxMMPBSA
gmxMMPBSA: command not found
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ conda install -c bioconda gromacs==2018.8 -y -q
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
- gromacs==2018.8
Current channels:
- https://conda.anaconda.org/bioconda/linux-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ amber.python -m pip install gmx_MMPBSA #
Error processing line 1 of /home/pglab-5000/Downloads/amber20/miniconda/lib/python3.9/site-packages/distutils-precedence.pth:
Traceback (most recent call last):
File "/home/pglab-5000/Downloads/amber20/miniconda/lib/python3.9/site.py", line 169, in addpackage
exec(line)
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named '_distutils_hack'
Remainder of file ignored
Defaulting to user installation because normal site-packages is not writeable
Collecting gmx_MMPBSA
Using cached gmx_MMPBSA-1.5.2-py3-none-any.whl (6.4 MB)
Collecting mpi4py>=3.1.3
Using cached mpi4py-3.1.3.tar.gz (2.5 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: pandas>=1.2.2 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from gmx_MMPBSA) (1.4.1)
Requirement already satisfied: matplotlib>=3.5.1 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from gmx_MMPBSA) (3.5.1)
Requirement already satisfied: scipy>=1.6.1 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from gmx_MMPBSA) (1.7.3)
Collecting h5py
Using cached h5py-3.6.0-cp39-cp39-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (4.5 MB)
Collecting seaborn>=0.11.2
Using cached seaborn-0.11.2-py3-none-any.whl (292 kB)
Requirement already satisfied: kiwisolver>=1.0.1 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (1.4.2)
Requirement already satisfied: fonttools>=4.22.0 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (4.32.0)
Requirement already satisfied: numpy>=1.17 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (1.21.5)
Requirement already satisfied: pillow>=6.2.0 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (9.1.0)
Requirement already satisfied: pyparsing>=2.2.1 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (3.0.4)
Requirement already satisfied: python-dateutil>=2.7 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (2.8.2)
Requirement already satisfied: cycler>=0.10 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (0.11.0)
Requirement already satisfied: packaging>=20.0 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (21.3)
Requirement already satisfied: pytz>=2020.1 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (2021.3)
Requirement already satisfied: six>=1.5 in ./Downloads/amber20/miniconda/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=3.5.1->gmx_MMPBSA) (1.16.0)
Building wheels for collected packages: mpi4py
Building wheel for mpi4py (pyproject.toml) ... done
Created wheel for mpi4py: filename=mpi4py-3.1.3-cp39-cp39-linux_x86_64.whl size=691686 sha256=3f6f60854eaa04c079001f887f929db05a99d753dce2706e699189279a7d6044
Stored in directory: /home/pglab-5000/.cache/pip/wheels/36/65/98/121355874b1b0cc974cecb5eb7d796be427257093f51796aba
Successfully built mpi4py
Installing collected packages: mpi4py, h5py, seaborn, gmx_MMPBSA
WARNING: The scripts gmx_MMPBSA, gmx_MMPBSA_ana and gmx_MMPBSA_test are installed in '/home/pglab-5000/.local/bin' which is not on PATH.
Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Successfully installed gmx_MMPBSA-1.5.2 h5py-3.6.0 mpi4py-3.1.3 seaborn-0.11.2
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ gmx_MMPBSA
gmx_MMPBSA: command not found
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ python -m pip install gmx_MMPBSA
Requirement already satisfied: gmx_MMPBSA in ./.local/lib/python3.9/site-packages (1.5.2)
Requirement already satisfied: matplotlib>=3.5.1 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from gmx_MMPBSA) (3.5.1)
Requirement already satisfied: seaborn>=0.11.2 in ./.local/lib/python3.9/site-packages (from gmx_MMPBSA) (0.11.2)
Requirement already satisfied: pandas>=1.2.2 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from gmx_MMPBSA) (1.4.2)
Requirement already satisfied: h5py in ./.local/lib/python3.9/site-packages (from gmx_MMPBSA) (3.6.0)
Requirement already satisfied: mpi4py>=3.1.3 in ./.local/lib/python3.9/site-packages (from gmx_MMPBSA) (3.1.3)
Requirement already satisfied: scipy>=1.6.1 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from gmx_MMPBSA) (1.8.0)
Requirement already satisfied: python-dateutil>=2.7 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (2.8.2)
Requirement already satisfied: packaging>=20.0 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (21.3)
Requirement already satisfied: kiwisolver>=1.0.1 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (1.4.2)
Requirement already satisfied: pillow>=6.2.0 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (9.0.1)
Requirement already satisfied: numpy>=1.17 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (1.22.3)
Requirement already satisfied: cycler>=0.10 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (0.11.0)
Requirement already satisfied: fonttools>=4.22.0 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (4.32.0)
Requirement already satisfied: pyparsing>=2.2.1 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from matplotlib>=3.5.1->gmx_MMPBSA) (3.0.8)
Requirement already satisfied: pytz>=2020.1 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from pandas>=1.2.2->gmx_MMPBSA) (2022.1)
Requirement already satisfied: six>=1.5 in ./miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib>=3.5.1->gmx_MMPBSA) (1.16.0)
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ gmx_MMPBSA
gmx_MMPBSA: command not found
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Collecting git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
Cloning https://github.com/Valdes-Tresanco-MS/ParmEd.git (to revision v3.4) to /tmp/pip-req-build-8q6odmkv
Running command git clone -q https://github.com/Valdes-Tresanco-MS/ParmEd.git /tmp/pip-req-build-8q6odmkv
Running command git checkout -b v3.4 --track origin/v3.4
Switched to a new branch 'v3.4'
Branch 'v3.4' set up to track remote branch 'v3.4' from 'origin'.
Resolved https://github.com/Valdes-Tresanco-MS/ParmEd.git to commit a195c7ec07b22da09678c5562367f44a068bce19
Building wheels for collected packages: ParmEd
Building wheel for ParmEd (setup.py) ... done
Created wheel for ParmEd: filename=ParmEd-3.4.3+10.ga195c7ec-cp39-cp39-linux_x86_64.whl size=609021 sha256=3bee7a8b8dbe0d132c48fdb2671f21f9461b93c4819b516dac469b4914235c8f
Stored in directory: /tmp/pip-ephem-wheel-cache-le5kx9p0/wheels/e7/0b/5c/198349ea05b0367406f9fda6909acc2ff1224760e0dd291ec4
Successfully built ParmEd
Installing collected packages: ParmEd
Attempting uninstall: ParmEd
Found existing installation: ParmEd 3.4.1
ERROR: Cannot uninstall 'ParmEd'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$ conda list
# packages in environment at /home/pglab-5000/miniconda3/envs/gmxMMPBSA:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
ambertools 21.12 py39hc630cb1_0 conda-forge
amberutils 21.0 pypi_0 pypi
arpack 3.7.0 hdefa2d7_2 conda-forge
binutils 2.35.1 hdd6e379_2 conda-forge
binutils_impl_linux-64 2.35.1 h27ae35d_9
binutils_linux-64 2.35 h67ddf6f_30 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
brotli 1.0.9 h166bdaf_7 conda-forge
brotli-bin 1.0.9 h166bdaf_7 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
c-compiler 1.2.0 h7f98852_0 conda-forge
ca-certificates 2021.10.8 ha878542_0 conda-forge
certifi 2021.10.8 py39hf3d152e_2 conda-forge
compilers 1.2.0 ha770c72_0 conda-forge
curl 7.82.0 h7bff187_0 conda-forge
cxx-compiler 1.2.0 h4bd325d_0 conda-forge
cycler 0.11.0 pyhd8ed1ab_0 conda-forge
cython 0.29.28 py39h5a03fae_2 conda-forge
fftw 3.3.10 nompi_h77c792f_102 conda-forge
fonttools 4.32.0 py39hb9d737c_0 conda-forge
fortran-compiler 1.2.0 h1990efc_0 conda-forge
freetype 2.10.4 h0708190_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gcc_impl_linux-64 9.3.0 h6df7d76_17
gcc_linux-64 9.3.0 hf25ea35_30 conda-forge
gfortran_impl_linux-64 9.3.0 hc4a2995_19 conda-forge
gfortran_linux-64 9.3.0 hdc58fab_30 conda-forge
giflib 5.2.1 h36c2ea0_2 conda-forge
gxx_impl_linux-64 9.3.0 hbdd7822_17
gxx_linux-64 9.3.0 h3fbe746_30 conda-forge
hdf4 4.2.15 h10796ff_3 conda-forge
hdf5 1.12.1 nompi_h2750804_103 conda-forge
icu 70.1 h27087fc_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 1.4.2 py39hf939315_1 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.12 hddcbb42_0 conda-forge
ld_impl_linux-64 2.35.1 h7274673_9
lerc 3.0 h9c3ff4c_0 conda-forge
libblas 3.9.0 13_linux64_openblas conda-forge
libbrotlicommon 1.0.9 h166bdaf_7 conda-forge
libbrotlidec 1.0.9 h166bdaf_7 conda-forge
libbrotlienc 1.0.9 h166bdaf_7 conda-forge
libcblas 3.9.0 13_linux64_openblas conda-forge
libcurl 7.82.0 h7bff187_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 3.3 he6710b0_2
libgcc-devel_linux-64 9.3.0 hb95220a_17
libgcc-ng 11.2.0 h1d223b6_15 conda-forge
libgfortran-ng 9.4.0 h69a702a_15 conda-forge
libgfortran5 9.4.0 h62347ff_15 conda-forge
libgomp 11.2.0 h1d223b6_15 conda-forge
libimagequant 2.17.0 h7f98852_1 conda-forge
liblapack 3.9.0 13_linux64_openblas conda-forge
libnetcdf 4.8.1 nompi_hb3fd0d9_101 conda-forge
libnghttp2 1.47.0 h727a467_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
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-devel_linux-64 9.3.0 hf0c5c8d_17
libstdcxx-ng 11.2.0 he4da1e4_15 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 h4de3113_1 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
lz4-c 1.9.3 h9c3ff4c_1 conda-forge
matplotlib-base 3.5.1 py39h2fa2bec_0 conda-forge
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 h7f8727e_2
netcdf-fortran 4.5.4 nompi_h2b6e579_100 conda-forge
numpy 1.22.3 py39h18676bf_2 conda-forge
openjpeg 2.4.0 hb52868f_1 conda-forge
openmpi 4.1.2 hbfc84c5_0 conda-forge
openssl 1.1.1n h166bdaf_0 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 1.4.2 py39h1832856_1 conda-forge
parmed 3.4.3 py39h5a03fae_2 conda-forge
perl 5.32.1 2_h7f98852_perl5 conda-forge
pillow 9.0.1 py39he69867a_1 conda-forge
pip 21.2.4 py39h06a4308_0
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyparsing 3.0.8 pyhd8ed1ab_0 conda-forge
pyqt5 5.15.6 pypi_0 pypi
pyqt5-qt5 5.15.2 pypi_0 pypi
pyqt5-sip 12.10.1 pypi_0 pypi
python 3.9.12 h12debd9_0
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 2022.1 pyhd8ed1ab_0 conda-forge
readline 8.1.2 h7f8727e_1
sander 16.0 pypi_0 pypi
scipy 1.8.0 py39hee8e79c_1 conda-forge
setuptools 61.2.0 py39h06a4308_0
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.38.2 hc218d9a_0
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tk 8.6.11 h1ccaba5_0
tzdata 2022a hda174b7_0
unicodedata2 14.0.0 py39hb9d737c_1 conda-forge
wheel 0.37.1 pyhd3eb1b0_0
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 h7b6447c_0
zlib 1.2.11 h166bdaf_1014 conda-forge
zstd 1.5.2 ha95c52a_0 conda-forge
(gmxMMPBSA) pglab-5000@pglab6000-lenovo-p520:~$
--
Thanks & Regards
_______________________________________________________
| |||||||||||||||||||||||
Navneet Kumar
Apr 16, 2022, 1:01:49 PM4/16/22
to gmx_MMPBSA
Mario Sergio Valdes
Apr 16, 2022, 1:38:18 PM4/16/22
to gmx_MMPBSA
You are mixing the installation methods. If you will do this using a conda environment, then you should not use amber.python. If you are going to use an AmberTools compilation, then you do not need to create a conda environment.
As far as I can see, you mixed up all the installation methods. Please follow these instructions.
1- Remove the gmx_MMPBSA installation from the system's python (./.local/lib/python3.9/site-packages)
As far as I can see, you mixed up all the installation methods. Please follow these instructions.
1- Remove the gmx_MMPBSA installation from the system's python (./.local/lib/python3.9/site-packages)
- Deactivate any active conda environment (conda deactivate) until none is displayed on the prompt.
- Then execute python -m pip uninstall gmx_MMPBSA. If it does not appear, uninstall it or it gives you an error, verify that there is no module in the address I indicated. If there is one, manually delete everything that contains gmx_MMPBSA or GMXMMPBSA in the name
2- Decide which method to use for the installation (conda environment or AmberTools compilation).
3- Remove the conda environment. Deactivate the gmxMMPBSA environment and execute conda env remove -n gmxMMPBSA
4- Remove gmx_MMPBSA from AmberTools compilation. Execute amber.python -m pip uninstall gmx_MMPBSA. Don't worry if ends in an error
If you are going to use the AmberTools compilation
1- Update setuptools to avoid the error being displayed and correctly install the packages in the proper library directory. Execute amber.python -m pip install setuptools -U
2- Make sure you did the source /path_to_amber/amber.sh
3- Follow exactly the instructions shown in the documentation.
If you are going to use a conda environment
1- Make sure that the PYTHONPATH environment variable is not set. To check if it is assigned type echo $PYTHONPATH, to unset it unset PYTHONPATH
2- Follow exactly the instructions shown in the documentation.
3- Create an alias to make sure that every time you activate this environment everything is correct. Paste this line in your .bashrc
2- Decide which method to use for the installation (conda environment or AmberTools compilation).
3- Remove the conda environment. Deactivate the gmxMMPBSA environment and execute conda env remove -n gmxMMPBSA
4- Remove gmx_MMPBSA from AmberTools compilation. Execute amber.python -m pip uninstall gmx_MMPBSA. Don't worry if ends in an error
If you are going to use the AmberTools compilation
1- Update setuptools to avoid the error being displayed and correctly install the packages in the proper library directory. Execute amber.python -m pip install setuptools -U
2- Make sure you did the source /path_to_amber/amber.sh
3- Follow exactly the instructions shown in the documentation.
If you are going to use a conda environment
1- Make sure that the PYTHONPATH environment variable is not set. To check if it is assigned type echo $PYTHONPATH, to unset it unset PYTHONPATH
2- Follow exactly the instructions shown in the documentation.
3- Create an alias to make sure that every time you activate this environment everything is correct. Paste this line in your .bashrc
Basic configuration
alias act_gmxMMPBSA="conda activate gmxMMPBSA; unset PYTHONPATH"
Including specific Gromacs installation
alias act_gmxMMPBSA="source /home/mario/programs/gromacs2021.5/bin/GMXRC; conda activate gmxMMPBSA; unset PYTHONPATH"
If you have any problem with libraries in your OS (example Centos7)
alias act_gmxMMPBSA="source /home/mario/programs/gromacs2021.5/bin/GMXRC; export LD_LIBRARY_PATH=/home/mario/programs/miniconda3/envs/gmxMMPBSA/lib; conda activate gmxMMPBSA; unset PYTHONPATH"
To activate the gmxMMPBSA conda environment, type act_gmxMMPBSA in your terminal. Check that gmx_MMPBSA is installed (gmx_MMPBSA -v)
Let me know if this solved the problems.
Mario S.
Navneet Kumar
Apr 16, 2022, 2:51:27 PM4/16/22
to Mario Sergio Valdes, gmx_MMPBSA
Hi!
Thankyou for your reply.
Done with installation and testing. Thank You very much!
I was planning to perform CAS of protein system having two chains i.e. A and B. Chain A also consists of cofactor GDP which is present during simulation. I have a list of residues which needs to be mutated at chain A or Chain B. The whole trajectory is simulated using CHARMM36ff. How should I manipulate the toppar folder?
Topology file looks like this
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
GDP 1
SOL 62479
NA 21
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
GDP 1
SOL 62479
NA 21
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Mario Ernesto
Apr 16, 2022, 2:55:39 PM4/16/22
to Navneet Kumar, Mario Sergio Valdes, gmx_MMPBSA
This is the tutorial for systems prepared with charmm force field
And this is for alanine scanning:
Cheers!
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