Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
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imren bayıl
Apr 30, 2023, 7:08:19 PM4/30/23
to gmx_MMPBSA
I am trying to install gmx_MMPBSA ubuntu
I used these commands respectively.
sudo apt install openmpi-bin libopenmpi-dev openssh-client
sudo apt-get install python
sudo apt-get install python3-pip
sudo apt-get upgrade
sudo apt-get update
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
conda update conda
conda create -n gmxMMPBSA python=3.9 -y -q
conda activate gmxMMPBSA
conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q after this command
ı am getting this error
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 initial frozen solve. Retrying with flexible solve.
how to fix this error
Mario Sergio Valdes
Apr 30, 2023, 7:57:20 PM4/30/23
to gmx_MMPBSA
Please, try using the env.yml file described in the documentation (https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/installation/#requirements). Currently, must be compilers=1.2.0
imren bayıl
May 1, 2023, 7:15:25 AM5/1/23
to gmx_MMPBSA
hi,
I tried to install usng env.yml file but I got this error
conda env create -n gmxMMPBSA --file env.yml after this code
active environment : gmxMMPBSA
active env location : /home/imren/miniconda3/envs/gmxMMPBSA
shell level : 1
user config file : /home/imren/.condarc
populated config files : /home/imren/.condarc
conda version : 23.3.1
conda-build version : not installed
python version : 3.10.10.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.35=0
__linux=5.19.0=0
__unix=0=0
base environment : /home/imren/miniconda3 (writable)
conda av data dir : /home/imren/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/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
package cache : /home/imren/miniconda3/pkgs
/home/imren/.conda/pkgs
envs directories : /home/imren/miniconda3/envs
/home/imren/.conda/envs
platform : linux-64
user-agent : conda/23.3.1 requests/2.29.0 CPython/3.10.10 Linux/5.19.0-41-generic ubuntu/22.04.2 glibc/2.35
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]: y
Upload successful.
active env location : /home/imren/miniconda3/envs/gmxMMPBSA
shell level : 1
user config file : /home/imren/.condarc
populated config files : /home/imren/.condarc
conda version : 23.3.1
conda-build version : not installed
python version : 3.10.10.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.35=0
__linux=5.19.0=0
__unix=0=0
base environment : /home/imren/miniconda3 (writable)
conda av data dir : /home/imren/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/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
package cache : /home/imren/miniconda3/pkgs
/home/imren/.conda/pkgs
envs directories : /home/imren/miniconda3/envs
/home/imren/.conda/envs
platform : linux-64
user-agent : conda/23.3.1 requests/2.29.0 CPython/3.10.10 Linux/5.19.0-41-generic ubuntu/22.04.2 glibc/2.35
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]: y
Upload successful.
how to fix this error
1 Mayıs 2023 Pazartesi tarihinde saat 02:57:20 UTC+3 itibarıyla mariosergi...@gmail.com şunları yazdı:
imren bayıl
May 1, 2023, 8:37:00 AM5/1/23
to gmx_MMPBSA
1 Mayıs 2023 Pazartesi tarihinde saat 14:15:25 UTC+3 itibarıyla imren bayıl şunları yazdı:
imren bayıl
May 1, 2023, 10:46:03 AM5/1/23
to gmx_MMPBSA
hi,I tried install gmx_mmpbsa my other computer which include ubuntu app
gmx_MMPBSA_test -h after running this code
gmx_MMPBSA_test -h after running this code
This program is part of gmx_MMPBSA and will allow you to run various gmx_MMPBSA examples easily.
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Test options:
-t [{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,101} ...]
The level the test is going to be run at. Multiple systems and analysis can be run at the same time.
Nr. of Sys
* 0 16 All -- Run all examples (Can take a long time!!!)
* 1 13 Minimal -- Does a minimal test with a set of systems and analyzes
that show that gmx_MMPBSA runs correctly. Only exclude 3drism, nmode
protein-ligand MT because take a long time or are redundant
* 2 9 Fast -- Only the calculations that take a short time are run (Default)
[Systems]:
Slow Frames
* 3 . | 10 Protein-Ligand (Single trajectory approximation)
* 4 . | 10 Protein-Protein
* 5 . | 10 Protein-DNA
* 6 x | 4 Protein-Membrane
* 7 . | 10 Protein-Glycan
* 8 x | 4 Metalloprotein-Peptide
* 9 . | 10 Protein-DNA-RNA-IONs-Ligand
* 10 x | 4 Protein-Ligand (CHARMM force field)
* 11 x | 4 Protein-ligand complex in membrane with CHARMMff
[Analysis]:
Slow Frames
* 12 . | 10 Alanine Scanning
* 13 . | 10 Stability calculation
* 14 . | 10 Decomposition Analysis
* 15 . | 16 Interaction Entropy approximation
* 16 . | 10 Protein-Ligand (Multiple trajectory approximation)
* 17 x | 4 Entropy calculation using Normal Mode approximation
* 18 x | 4 Calculations using 3D-RISM approximation
-f FOLDER, --folder FOLDER
Defines the folder to store all data
-r, --reuse Defines the existing test forlder will be reuse
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-n NUM_PROCESSORS, --num_processors NUM_PROCESSORS
Defines the number of processor cores you want to use with MPI per calculation. If the number of frames is less than the number of cpus defined, the calculation will be performed withthe number of processors = number of frames
gmx_MMPBSA is an effort to implement the GB/PB and others calculations in GROMACS.
Based on MMPBSA.py (version 16.0) and AmberTools20
optional arguments:
-h, --help show this help message and exit
-v, --version show program's version number and exit
Test options:
-t [{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,101} ...]
The level the test is going to be run at. Multiple systems and analysis can be run at the same time.
Nr. of Sys
* 0 16 All -- Run all examples (Can take a long time!!!)
* 1 13 Minimal -- Does a minimal test with a set of systems and analyzes
that show that gmx_MMPBSA runs correctly. Only exclude 3drism, nmode
protein-ligand MT because take a long time or are redundant
* 2 9 Fast -- Only the calculations that take a short time are run (Default)
[Systems]:
Slow Frames
* 3 . | 10 Protein-Ligand (Single trajectory approximation)
* 4 . | 10 Protein-Protein
* 5 . | 10 Protein-DNA
* 6 x | 4 Protein-Membrane
* 7 . | 10 Protein-Glycan
* 8 x | 4 Metalloprotein-Peptide
* 9 . | 10 Protein-DNA-RNA-IONs-Ligand
* 10 x | 4 Protein-Ligand (CHARMM force field)
* 11 x | 4 Protein-ligand complex in membrane with CHARMMff
[Analysis]:
Slow Frames
* 12 . | 10 Alanine Scanning
* 13 . | 10 Stability calculation
* 14 . | 10 Decomposition Analysis
* 15 . | 16 Interaction Entropy approximation
* 16 . | 10 Protein-Ligand (Multiple trajectory approximation)
* 17 x | 4 Entropy calculation using Normal Mode approximation
* 18 x | 4 Calculations using 3D-RISM approximation
-f FOLDER, --folder FOLDER
Defines the folder to store all data
-r, --reuse Defines the existing test forlder will be reuse
-ng, --nogui No open gmx_MMPBSA_ana after all calculations finished
-n NUM_PROCESSORS, --num_processors NUM_PROCESSORS
Defines the number of processor cores you want to use with MPI per calculation. If the number of frames is less than the number of cpus defined, the calculation will be performed withthe number of processors = number of frames
gmx_MMPBSA is an effort to implement the GB/PB and others calculations in GROMACS.
Based on MMPBSA.py (version 16.0) and AmberTools20
Then I tried to run example which is protein-ligand/ST
gmx_MMPBSA -O -i mmpbsa.in -cs com.tpr -ct com_traj.xtc -ci index.ndx -cg 3 4 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv after writing code,
I am getting this error,
gmx_MMPBSA: error: unrecognized arguments: -cp topol.top I dont understand where I have done wrong
1 Mayıs 2023 Pazartesi tarihinde saat 15:37:00 UTC+3 itibarıyla imren bayıl şunları yazdı:
Mario Sergio Valdes
May 1, 2023, 1:08:34 PM5/1/23
to gmx_MMPBSA
Does the error look that the one below? If yes, probably is a network problem. Sometimes it is related to VPN connections
conda av metadata url : None
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]:
:~/Downloads$ conda env create -n gmxMMPBSA --file env.yml
Collecting package metadata (repodata.json): failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 761, in _update_chunk_length
self.chunk_left = int(line, 16)
ValueError: invalid literal for int() with base 16: b''
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 444, in _error_catcher
yield
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 828, in read_chunked
self._update_chunk_length()
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 765, in _update_chunk_length
raise InvalidChunkLength(self, line)
urllib3.exceptions.InvalidChunkLength: InvalidChunkLength(got length b'', 0 bytes read)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/models.py", line 816, in generate
yield from self.raw.stream(chunk_size, decode_content=True)
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 624, in stream
for line in self.read_chunked(amt, decode_content=decode_content):
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 857, in read_chunked
self._original_response.close()
File "/home/mario/miniconda3/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 461, in _error_catcher
raise ProtocolError("Connection broken: %r" % e, e)
urllib3.exceptions.ProtocolError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read)", InvalidChunkLength(got length b'', 0 bytes read))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1118, in __call__
return func(*args, **kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 78, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/notices/core.py", line 109, in wrapper
return func(*args, **kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 154, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda_env/installers/conda.py", line 49, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 136, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 179, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 284, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/common/io.py", line 84, in decorated
return f(*args, **kwds)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 451, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 1061, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/index.py", line 272, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 142, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "/home/mario/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 609, in result_iterator
yield fs.pop().result()
File "/home/mario/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 439, in result
return self.__get_result()
File "/home/mario/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
raise self._exception
File "/home/mario/miniconda3/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 131, in <lambda>
subdir_query = lambda url: tuple(
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 147, in query
self.load()
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 213, in load
_internal_state = self._load()
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 303, in _load
raw_repodata_str = fetch_repodata_remote_request(
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 571, in fetch_repodata_remote_request
resp = session.get(
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 600, in get
return self.request("GET", url, **kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 587, in request
resp = self.send(prep, **send_kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 745, in send
r.content
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/models.py", line 899, in content
self._content = b"".join(self.iter_content(CONTENT_CHUNK_SIZE)) or b""
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/models.py", line 818, in generate
raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read)", InvalidChunkLength(got length b'', 0 bytes read))
`$ /home/mario/miniconda3/bin/conda-env create -n gmxMMPBSA --file env.yml`
environment variables:
CIO_TEST=<not set>
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/mario/miniconda3/bin/conda
CONDA_PREFIX=/home/mario/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/mario/miniconda3/bin/python
CONDA_ROOT=/home/mario/miniconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
LD_PRELOAD=<not set>
PATH=/home/mario/.rbenv/shims:/home/mario/.rbenv/bin:/home/mario/miniconda3
/bin:/home/mario/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/u
sr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/sna
p/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
WINDOWPATH=2
active environment : base
active env location : /home/mario/miniconda3
shell level : 1
user config file : /home/mario/.condarc
populated config files :
conda version : 22.11.1
conda-build version : not installed
python version : 3.9.15.final.0
virtual packages : __archspec=1=x86_64
__cuda=11.4=0
__glibc=2.31=0
__linux=5.15.0=0
__unix=0=0
base environment : /home/mario/miniconda3 (writable)
conda av data dir : /home/mario/miniconda3/etc/conda
Collecting package metadata (repodata.json): failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 761, in _update_chunk_length
self.chunk_left = int(line, 16)
ValueError: invalid literal for int() with base 16: b''
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 444, in _error_catcher
yield
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 828, in read_chunked
self._update_chunk_length()
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 765, in _update_chunk_length
raise InvalidChunkLength(self, line)
urllib3.exceptions.InvalidChunkLength: InvalidChunkLength(got length b'', 0 bytes read)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/models.py", line 816, in generate
yield from self.raw.stream(chunk_size, decode_content=True)
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 624, in stream
for line in self.read_chunked(amt, decode_content=decode_content):
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 857, in read_chunked
self._original_response.close()
File "/home/mario/miniconda3/lib/python3.9/contextlib.py", line 137, in __exit__
self.gen.throw(typ, value, traceback)
File "/home/mario/miniconda3/lib/python3.9/site-packages/urllib3/response.py", line 461, in _error_catcher
raise ProtocolError("Connection broken: %r" % e, e)
urllib3.exceptions.ProtocolError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read)", InvalidChunkLength(got length b'', 0 bytes read))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/exceptions.py", line 1118, in __call__
return func(*args, **kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda_env/cli/main.py", line 78, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/notices/core.py", line 109, in wrapper
return func(*args, **kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda_env/cli/main_create.py", line 154, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda_env/installers/conda.py", line 49, in install
unlink_link_transaction = solver.solve_for_transaction(
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 136, in solve_for_transaction
unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 179, in solve_for_diff
final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 284, in solve_final_state
ssc = self._collect_all_metadata(ssc)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/common/io.py", line 84, in decorated
return f(*args, **kwds)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 451, in _collect_all_metadata
index, r = self._prepare(prepared_specs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/solve.py", line 1061, in _prepare
reduced_index = get_reduced_index(self.prefix, self.channels,
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/index.py", line 272, in get_reduced_index
new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 142, in query_all
result = tuple(concat(executor.map(subdir_query, channel_urls)))
File "/home/mario/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 609, in result_iterator
yield fs.pop().result()
File "/home/mario/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 439, in result
return self.__get_result()
File "/home/mario/miniconda3/lib/python3.9/concurrent/futures/_base.py", line 391, in __get_result
raise self._exception
File "/home/mario/miniconda3/lib/python3.9/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 131, in <lambda>
subdir_query = lambda url: tuple(
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 147, in query
self.load()
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 213, in load
_internal_state = self._load()
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 303, in _load
raw_repodata_str = fetch_repodata_remote_request(
File "/home/mario/miniconda3/lib/python3.9/site-packages/conda/core/subdir_data.py", line 571, in fetch_repodata_remote_request
resp = session.get(
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 600, in get
return self.request("GET", url, **kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 587, in request
resp = self.send(prep, **send_kwargs)
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/sessions.py", line 745, in send
r.content
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/models.py", line 899, in content
self._content = b"".join(self.iter_content(CONTENT_CHUNK_SIZE)) or b""
File "/home/mario/miniconda3/lib/python3.9/site-packages/requests/models.py", line 818, in generate
raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read)", InvalidChunkLength(got length b'', 0 bytes read))
`$ /home/mario/miniconda3/bin/conda-env create -n gmxMMPBSA --file env.yml`
environment variables:
CIO_TEST=<not set>
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/mario/miniconda3/bin/conda
CONDA_PREFIX=/home/mario/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/mario/miniconda3/bin/python
CONDA_ROOT=/home/mario/miniconda3
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
LD_PRELOAD=<not set>
PATH=/home/mario/.rbenv/shims:/home/mario/.rbenv/bin:/home/mario/miniconda3
/bin:/home/mario/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/u
sr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/sna
p/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
WINDOWPATH=2
active environment : base
active env location : /home/mario/miniconda3
shell level : 1
user config file : /home/mario/.condarc
populated config files :
conda version : 22.11.1
conda-build version : not installed
python version : 3.9.15.final.0
virtual packages : __archspec=1=x86_64
__cuda=11.4=0
__glibc=2.31=0
__linux=5.15.0=0
__unix=0=0
base environment : /home/mario/miniconda3 (writable)
conda av data dir : /home/mario/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
package cache : /home/mario/miniconda3/pkgs
/home/mario/.conda/pkgs
envs directories : /home/mario/miniconda3/envs
/home/mario/.conda/envs
platform : linux-64
user-agent : conda/22.11.1 requests/2.28.1 CPython/3.9.15 Linux/5.15.0-71-generic zorin/16.2 glibc/2.31
/home/mario/.conda/pkgs
envs directories : /home/mario/miniconda3/envs
/home/mario/.conda/envs
platform : linux-64
user-agent : conda/22.11.1 requests/2.28.1 CPython/3.9.15 Linux/5.15.0-71-generic zorin/16.2 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Would you like conda to send this report to the core maintainers? [y/N]:
Timeout reached. No report sent.
marioe911116
May 1, 2023, 1:40:58 PM5/1/23
to gmx_MMPBSA
can you try to run this command:
gmx_MMPBSA_test -t 3 -f /path_to_folder_where_you_want_the_files_to_downloaded
gmx_MMPBSA_test -t 3 -f /path_to_folder_where_you_want_the_files_to_downloaded
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