Hello all please help me for gromacs installation with cuda. I m getting following error

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question anand@anand-OMEN-by-HP-Gaming-Laptop-16-wf1xxx:~/sim1/gromacs-2024.4/build$ cmake … -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
– Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Development Development.Module Development.Embed) (found suitable version “3.12.3”, minimum required is “3.7”)
– Checking if nvcc accepts flags --generate-code=arch=compute_35,code=sm_35
– Checking if nvcc accepts flags --generate-code=arch=compute_35,code=sm_35 - No
– Checking if nvcc accepts flags --generate-code=arch=compute_37,code=sm_37
– Checking if nvcc accepts flags --generate-code=arch=compute_37,code=sm_37 - No
CMake Error at /usr/share/cmake-3.28/Modules/Internal/CMakeCUDAArchitecturesValidate.cmake:7 (message):
CMAKE_CUDA_ARCHITECTURES must be non-empty if set.
Call Stack (most recent call first):
/usr/share/cmake-3.28/Modules/CMakeDetermineCUDACompiler.cmake:116 (cmake_cuda_architectures_validate)
cmake/gmxManageCuda.cmake:116 (enable_language)
CMakeLists.txt:700 (include)

– Configuring incomplete, errors occurred!
anand@anand-OMEN-by-HP-Gaming-Laptop-16-wf1xxx:~/sim1/gromacs-2024.4/build$

2

Hi!

Could you fully share the log (so we know compiler versions etc) and how CUDA was installed?

Can you try adding -DCMAKE_CUDA_ARCHITECTURES=native you your cmake call to see if it helps?

3

Thanks, its working using this following command
cmake … -DCMAKE_CUDA_ARCHITECTURES=native
Now my question is would I get gpu support for acceleration?

4

Now my question is would I get gpu support for acceleration?

Yes. But you should use the new flag in addition to the ones you have.

5

Sir after this command it showed gromacs installation complete but gpu support still disabled and then thereafter ubantu screen was stuck in hanging mode for long time. Now my laptop is not opening Ubantu 24.04 lts. what should I do now to recover Ubantu in my system?

6

If you compiled GROMACS with -DGMX_GPU=CUDA, then it will have CUDA support enabled. Perhaps you have some old version installed in a different directory and it gets picked up instead of the newly-installed one?

In some rare cases GROMACS can cause the system to hang (usually happens if there’s poor cooling or some other factors), but there is nothing GROMACS does that can prevent the system from booting. If your laptop cannot boot into the operating system, the problem is not related to GROMACS.

1 Like
7

issue resolved. now I have successfully installed gromacs.
Now performing md simulation but facing this issue. So please help.

Welcome to Ubuntu 22.04.5 LTS (GNU/Linux 5.10.16.3-microsoft-standard-WSL2 x86_64)

System information as of Sun Dec 1 05:10:36 IST 2024

System load: 0.0 Processes: 9
Usage of /: 10.2% of 250.98GB Users logged in: 0
Memory usage: 2% IPv4 address for eth0: 172.25.125.71
Swap usage: 0%

This message is shown once a day. To disable it please create the
/root/.hushlogin file.
root@LAPTOP-45V3UM01:~# sudo apt update
Get:1 file:/var/cuda-repo-wsl-ubuntu-12-6-local InRelease [1572 B]
Get:1 file:/var/cuda-repo-wsl-ubuntu-12-6-local InRelease [1572 B]
Hit:2 http://security.ubuntu.com/ubuntu jammy-security InRelease
Hit:3 http://archive.ubuntu.com/ubuntu jammy InRelease
Hit:4 http://archive.ubuntu.com/ubuntu jammy-updates InRelease
Hit:5 http://archive.ubuntu.com/ubuntu jammy-backports InRelease
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
All packages are up to date.
root@LAPTOP-45V3UM01:~# sudo apt upgrade
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
Calculating upgrade… Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
root@LAPTOP-45V3UM01:~# sudo apt install build-essential
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
build-essential is already the newest version (12.9ubuntu3).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
root@LAPTOP-45V3UM01:~# gcc --version
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

root@LAPTOP-45V3UM01:~# g++ --version
g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Copyright (C) 2021 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

root@LAPTOP-45V3UM01:~# gedit newfile

(gedit:438): Gtk-WARNING **: 05:12:07.055: cannot open display:
root@LAPTOP-45V3UM01:~# gedit newfile.c

(gedit:440): Gtk-WARNING **: 05:12:30.224: cannot open display:
root@LAPTOP-45V3UM01:~# source /usr/local/gromacs/bin/GMXRC
root@LAPTOP-45V3UM01:~# gmx
:-) GROMACS - gmx, 2024.4 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /root
Command line:
gmx

SYNOPSIS

gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice ]
[-[no]backup]

OPTIONS

Other options:

-[no]h (no)
Print help and quit
-[no]quiet (no)
Do not print common startup info or quotes
-[no]version (no)
Print extended version information and quit
-[no]copyright (no)
Print copyright information on startup
-nice (19)
Set the nicelevel (default depends on command)
-[no]backup (yes)
Write backups if output files exist

Additional help is available on the following topics:
commands List of available commands
selections Selection syntax and usage
To access the help, use ‘gmx help ’.
For help on a command, use ‘gmx help ’.

GROMACS reminds you: “Make the Floor Burn” (2 Unlimited)

root@LAPTOP-45V3UM01:~# gmx --version
:-) GROMACS - gmx, 2024.4 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /root
Command line:
gmx --version

GROMACS version: 2024.4
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: CUDA
NBNxM GPU setup: super-cluster 2x2x2 / cluster 8
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library: cuFFT
Multi-GPU FFT: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 11.4.0
C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 11.4.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
BLAS library: Internal
LAPACK library: Internal
CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2024 NVIDIA Corporation;Built on Tue_Oct_29_23:50:19_PDT_2024;Cuda compilation tools, release 12.6, V12.6.85;Build cuda_12.6.r12.6/compiler.35059454_0
CUDA compiler flags:-std=c++17;–generate-code=arch=compute_50,code=sm_50;–generate-code=arch=compute_52,code=sm_52;–generate-code=arch=compute_60,code=sm_60;–generate-code=arch=compute_61,code=sm_61;–generate-code=arch=compute_70,code=sm_70;–generate-code=arch=compute_75,code=sm_75;–generate-code=arch=compute_80,code=sm_80;–generate-code=arch=compute_86,code=sm_86;–generate-code=arch=compute_89,code=sm_89;–generate-code=arch=compute_90,code=sm_90;-Wno-deprecated-gpu-targets;–generate-code=arch=compute_53,code=sm_53;–generate-code=arch=compute_80,code=sm_80;-use_fast_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;-D_FORCE_INLINES;-Xcompiler;-fopenmp;-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict -fopenmp -O3 -DNDEBUG
CUDA driver: 12.50
CUDA runtime: 12.60

root@LAPTOP-45V3UM01:~# obabel
Command ‘obabel’ not found, but can be installed with:
apt install openbabel
root@LAPTOP-45V3UM01:~# sudo apt install openbabel
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
The following additional packages will be installed:
libboost-iostreams1.74.0 libinchi1 libmaeparser1 libopenbabel7
The following NEW packages will be installed:
libboost-iostreams1.74.0 libinchi1 libmaeparser1 libopenbabel7 openbabel
0 upgraded, 5 newly installed, 0 to remove and 0 not upgraded.
Need to get 4148 kB of archives.
After this operation, 19.1 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://archive.ubuntu.com/ubuntu jammy/main amd64 libboost-iostreams1.74.0 amd64 1.74.0-14ubuntu3 [245 kB]
Get:2 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libinchi1 amd64 1.03+dfsg-4 [455 kB]
Get:3 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libmaeparser1 amd64 1.2.4-1build1 [88.2 kB]
Get:4 http://archive.ubuntu.com/ubuntu jammy/universe amd64 libopenbabel7 amd64 3.1.1+dfsg-6ubuntu5 [3231 kB]
Get:5 http://archive.ubuntu.com/ubuntu jammy/universe amd64 openbabel amd64 3.1.1+dfsg-6ubuntu5 [128 kB]
Fetched 4148 kB in 5s (842 kB/s)
Selecting previously unselected package libboost-iostreams1.74.0:amd64.
(Reading database … 96011 files and directories currently installed.)
Preparing to unpack …/libboost-iostreams1.74.0_1.74.0-14ubuntu3_amd64.deb …
Unpacking libboost-iostreams1.74.0:amd64 (1.74.0-14ubuntu3) …
Selecting previously unselected package libinchi1.
Preparing to unpack …/libinchi1_1.03+dfsg-4_amd64.deb …
Unpacking libinchi1 (1.03+dfsg-4) …
Selecting previously unselected package libmaeparser1:amd64.
Preparing to unpack …/libmaeparser1_1.2.4-1build1_amd64.deb …
Unpacking libmaeparser1:amd64 (1.2.4-1build1) …
Selecting previously unselected package libopenbabel7.
Preparing to unpack …/libopenbabel7_3.1.1+dfsg-6ubuntu5_amd64.deb …
Unpacking libopenbabel7 (3.1.1+dfsg-6ubuntu5) …
Selecting previously unselected package openbabel.
Preparing to unpack …/openbabel_3.1.1+dfsg-6ubuntu5_amd64.deb …
Unpacking openbabel (3.1.1+dfsg-6ubuntu5) …
Setting up libboost-iostreams1.74.0:amd64 (1.74.0-14ubuntu3) …
Setting up libmaeparser1:amd64 (1.2.4-1build1) …
Setting up libinchi1 (1.03+dfsg-4) …
Setting up libopenbabel7 (3.1.1+dfsg-6ubuntu5) …
Setting up openbabel (3.1.1+dfsg-6ubuntu5) …
Processing triggers for libc-bin (2.35-0ubuntu3.8) …
/sbin/ldconfig.real: Can’t link /usr/lib/wsl/lib/libnvoptix_loader.so.1 to libnvoptix.so.1
Processing triggers for man-db (2.10.2-1) …
root@LAPTOP-45V3UM01:~# obabel
No input file or format spec or possibly a misplaced option.
Most options must come after the input files. (-i -o -O -m can be anywhwere.)

Open Babel 3.1.1 – Feb 7 2022 – 06:51:49
Usage:
obabel [-i] [-o] -O [Options]
Try -H option for more information.
root@LAPTOP-45V3UM01:~# pip install networks==2.3
Command ‘pip’ not found, but can be installed with:
apt install python3-pip
root@LAPTOP-45V3UM01:~# sudo apt install python3-pip
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
The following additional packages will be installed:
libexpat1-dev libpython3-dev libpython3.10-dev python3-dev python3-wheel python3.10-dev zlib1g-dev
The following NEW packages will be installed:
libexpat1-dev libpython3-dev libpython3.10-dev python3-dev python3-pip python3-wheel python3.10-dev
zlib1g-dev
0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded.
Need to get 6951 kB of archives.
After this operation, 30.4 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libexpat1-dev amd64 2.4.7-1ubuntu0.4 [147 kB]
Get:2 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu9.2 [164 kB]
Get:3 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libpython3.10-dev amd64 3.10.12-1~22.04.7 [4762 kB]
Get:4 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 libpython3-dev amd64 3.10.6-1~22.04.1 [7064 B]
Get:5 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 python3.10-dev amd64 3.10.12-1~22.04.7 [508 kB]
Get:6 http://archive.ubuntu.com/ubuntu jammy-updates/main amd64 python3-dev amd64 3.10.6-1~22.04.1 [26.0 kB]
Get:7 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 python3-wheel all 0.37.1-2ubuntu0.22.04.1 [32.0 kB]
Get:8 http://archive.ubuntu.com/ubuntu jammy-updates/universe amd64 python3-pip all 22.0.2+dfsg-1ubuntu0.5 [1306 kB]
Fetched 6951 kB in 9s (809 kB/s)
Selecting previously unselected package libexpat1-dev:amd64.
(Reading database … 96268 files and directories currently installed.)
Preparing to unpack …/0-libexpat1-dev_2.4.7-1ubuntu0.4_amd64.deb …
Unpacking libexpat1-dev:amd64 (2.4.7-1ubuntu0.4) …
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack …/1-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu9.2_amd64.deb …
Unpacking zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9.2) …
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Preparing to unpack …/2-libpython3.10-dev_3.10.12-1~22.04.7_amd64.deb …
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Unpacking python3-dev (3.10.6-1~22.04.1) …
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Preparing to unpack …/6-python3-wheel_0.37.1-2ubuntu0.22.04.1_all.deb …
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Preparing to unpack …/7-python3-pip_22.0.2+dfsg-1ubuntu0.5_all.deb …
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Setting up python3-wheel (0.37.1-2ubuntu0.22.04.1) …
Setting up libexpat1-dev:amd64 (2.4.7-1ubuntu0.4) …
Setting up python3-pip (22.0.2+dfsg-1ubuntu0.5) …
Setting up zlib1g-dev:amd64 (1:1.2.11.dfsg-2ubuntu9.2) …
Setting up libpython3.10-dev:amd64 (3.10.12-1~22.04.7) …
Setting up python3.10-dev (3.10.12-1~22.04.7) …
Setting up libpython3-dev:amd64 (3.10.6-1~22.04.1) …
Setting up python3-dev (3.10.6-1~22.04.1) …
Processing triggers for man-db (2.10.2-1) …
root@LAPTOP-45V3UM01:~# pip install networkx==2.3
Collecting networkx==2.3
Downloading networkx-2.3.zip (1.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 4.8 MB/s eta 0:00:00
Preparing metadata (setup.py) … done
Collecting decorator>=4.3.0
Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Building wheels for collected packages: networkx
Building wheel for networkx (setup.py) … done
Created wheel for networkx: filename=networkx-2.3-py2.py3-none-any.whl size=1556007 sha256=c73126b647e2193003c4f9d3b8e66fc6feefda82f408de00477be2300f29df7c
Stored in directory: /root/.cache/pip/wheels/a2/61/d8/147fad6a09bfd85366862c93d34556b9e155ce7690f8c0aa13
Successfully built networkx
Installing collected packages: decorator, networkx
Successfully installed decorator-5.1.1 networkx-2.3
WARNING: Running pip as the ‘root’ user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv
root@LAPTOP-45V3UM01:~# obabel jz4.pdb -O jz4.mol2 -h

8

Hi. Could you explain what the issue is? Your log shows some steps of the installation, which seem to proceed successfully (albeit, with warnings: it’s indeed a bad practice to run things as root), but nothing wrong there as far as I can see.

9

tomcat@LAPTOP-45V3UM01:~ sudo apt update [sudo] password for tomcat: Get:1 file:/var/cuda-repo-wsl-ubuntu-12-6-local InRelease [1572 B] Get:1 file:/var/cuda-repo-wsl-ubuntu-12-6-local InRelease [1572 B] Get:2 [http://security.ubuntu.com/ubuntu](http://security.ubuntu.com/ubuntu) noble-security InRelease [126 kB] Hit:3 [https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu](https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu) noble InRelease Get:4 [http://security.ubuntu.com/ubuntu](http://security.ubuntu.com/ubuntu) noble-security/main amd64 Packages [498 kB] Hit:5 [http://archive.ubuntu.com/ubuntu](http://archive.ubuntu.com/ubuntu) noble InRelease Get:6 [http://archive.ubuntu.com/ubuntu](http://archive.ubuntu.com/ubuntu) noble-updates InRelease [126 kB] Get:7 [http://security.ubuntu.com/ubuntu](http://security.ubuntu.com/ubuntu) noble-security/universe amd64 Packages [562 kB] Hit:8 [http://archive.ubuntu.com/ubuntu](http://archive.ubuntu.com/ubuntu) noble-backports InRelease Fetched 1312 kB in 3s (378 kB/s) Reading package lists... Done Building dependency tree... Done Reading state information... Done All packages are up to date. tomcat@LAPTOP-45V3UM01:~ sudo apt upgrade
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
Calculating upgrade… Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
tomcat@LAPTOP-45V3UM01:~ sudo apt build-essential E: Invalid operation build-essential tomcat@LAPTOP-45V3UM01:~ sudo apt install build-essential
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
build-essential is already the newest version (12.10ubuntu1).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
tomcat@LAPTOP-45V3UM01:~ source /usr/local/gromacs/bin/GMXRC tomcat@LAPTOP-45V3UM01:~ gmx --version
:-) GROMACS - gmx, 2024.4 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/tomcat
Command line:
gmx --version

GROMACS version: 2024.4
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: CUDA
NBNxM GPU setup: super-cluster 2x2x2 / cluster 8
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library: cuFFT
Multi-GPU FFT: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 13.2.0
C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 13.2.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG
BLAS library: Internal
LAPACK library: Internal
CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2024 NVIDIA Corporation;Built on Tue_Oct_29_23:50:19_PDT_2024;Cuda compilation tools, release 12.6, V12.6.85;Build cuda_12.6.r12.6/compiler.35059454_0
CUDA compiler flags:-std=c++17;–generate-code=arch=compute_50,code=sm_50;–generate-code=arch=compute_52,code=sm_52;–generate-code=arch=compute_60,code=sm_60;–generate-code=arch=compute_61,code=sm_61;–generate-code=arch=compute_70,code=sm_70;–generate-code=arch=compute_75,code=sm_75;–generate-code=arch=compute_80,code=sm_80;–generate-code=arch=compute_86,code=sm_86;–generate-code=arch=compute_89,code=sm_89;–generate-code=arch=compute_90,code=sm_90;-Wno-deprecated-gpu-targets;–generate-code=arch=compute_53,code=sm_53;–generate-code=arch=compute_80,code=sm_80;-use_fast_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;-D_FORCE_INLINES;-Xcompiler;-fopenmp;-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG
CUDA driver: 12.50
CUDA runtime: 12.60

tomcat@LAPTOP-45V3UM01:~ ls cuda-repo-wsl-ubuntu-12-6-local_12.6.3-1_amd64.deb fftw-3.3.10.tar.gz:Zone.Identifier simgupta5with3hqd fftw-3.3.10 gromacs-2024.4 fftw-3.3.10.tar.gz gromacs-2024.4.tar.gz tomcat@LAPTOP-45V3UM01:~ cd simgupta5with3hqd/
tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ ls
3hqd.pdb cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier jz4.pdb:Zone.Identifier
3hqd_clean.pdb charmm36-jul2022.ff posre.itp
3hqd_processed.gro charmm36-jul2022.ff.tgz sort_mol2_bonds.pl
JZ4.mol2 charmm36-jul2022.ff.tgz:Zone.Identifier topol.top
cgenff_charmm2gmx_py3_nx2.py jz4.pdb
tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ perl sort_mol2_bonds.pl JZ4.mol2 jz4_fix.mol2
Found 47 atoms in the molecule, with 49 bonds.
tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ ls
3hqd.pdb cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier jz4.pdb:Zone.Identifier
3hqd_clean.pdb charmm36-jul2022.ff jz4_fix.mol2
3hqd_processed.gro charmm36-jul2022.ff.tgz posre.itp
JZ4.mol2 charmm36-jul2022.ff.tgz:Zone.Identifier sort_mol2_bonds.pl
cgenff_charmm2gmx_py3_nx2.py jz4.pdb topol.top
tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ ls
3hqd.pdb charmm36-jul2022.ff jz4_fix.str
3hqd_clean.pdb charmm36-jul2022.ff.tgz posre.itp
3hqd_processed.gro charmm36-jul2022.ff.tgz:Zone.Identifier sort_mol2_bonds.pl
JZ4.mol2 jz4.pdb topol.top
cgenff_charmm2gmx_py3_nx2.py jz4.pdb:Zone.Identifier
cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier jz4_fix.mol2
tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ python3 cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_fix.mol2 jz4_fix.str charmm36-j
ul2022.ff
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:62: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:69: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:132: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:143: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:168: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:185: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:581: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:585: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:606: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:622: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:646: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:869: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:896: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
Traceback (most recent call last):
File “/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py”, line 53, in
import numpy as np
ModuleNotFoundError: No module named ‘numpy’
tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ cd ~
tomcat@LAPTOP-45V3UM01:~$ python3
Python 3.12.3 (main, Nov 6 2024, 18:32:19) [GCC 13.2.0] on linux
Type “help”, “copyright”, “credits” or “license” for more information.

tomcat@LAPTOP-45V3UM01:~ sudo apt install python3-pip [sudo] password for tomcat: Reading package lists... Done Building dependency tree... Done Reading state information... Done python3-pip is already the newest version (24.0+dfsg-1ubuntu1.1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. tomcat@LAPTOP-45V3UM01:~ pip3 install numpy
error: externally-managed-environment

× This environment is externally managed
╰─> To install Python packages system-wide, try apt install
python3-xyz, where xyz is the package you are trying to
install.

If you wish to install a non-Debian-packaged Python package,
create a virtual environment using python3 -m venv path/to/venv.
Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make
sure you have python3-full installed.

If you wish to install a non-Debian packaged Python application,
it may be easiest to use pipx install xyz, which will manage a
virtual environment for you. Make sure you have pipx installed.

See /usr/share/doc/python3.12/README.venv for more information.

note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages.
hint: See PEP 668 for the detailed specification.
tomcat@LAPTOP-45V3UM01:~$ python3 -m venv .venv
The virtual environment was not created successfully because ensurepip is not
available. On Debian/Ubuntu systems, you need to install the python3-venv
package using the following command.

apt install python3.12-venv

You may need to use sudo with that command. After installing the python3-venv
package, recreate your virtual environment.

Failing command: /home/tomcat/.venv/bin/python3

tomcat@LAPTOP-45V3UM01:~ sudo apt install python3.12-venv [sudo] password for tomcat: Reading package lists... Done Building dependency tree... Done Reading state information... Done The following NEW packages will be installed: python3.12-venv 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 5678 B of archives. After this operation, 28.7 kB of additional disk space will be used. Get:1 [http://archive.ubuntu.com/ubuntu](http://archive.ubuntu.com/ubuntu) noble-updates/universe amd64 python3.12-venv amd64 3.12.3-1ubuntu0.3 [5678 B] Fetched 5678 B in 1s (7995 B/s) Selecting previously unselected package python3.12-venv. (Reading database ... 68893 files and directories currently installed.) Preparing to unpack .../python3.12-venv_3.12.3-1ubuntu0.3_amd64.deb ... Unpacking python3.12-venv (3.12.3-1ubuntu0.3) ... Setting up python3.12-venv (3.12.3-1ubuntu0.3) ... tomcat@LAPTOP-45V3UM01:~ python3 -m venv .venv
tomcat@LAPTOP-45V3UM01:~ source .venv/bin/activate (.venv) tomcat@LAPTOP-45V3UM01:~ pip3 install numpy
Collecting numpy
Downloading numpy-2.1.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.0/62.0 kB 1.9 MB/s eta 0:00:00
Downloading numpy-2.1.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.0/16.0 MB 8.9 MB/s eta 0:00:00
Installing collected packages: numpy
Successfully installed numpy-2.1.3
(.venv) tomcat@LAPTOP-45V3UM01:~ python3 cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_fix.mol2 jz4_fix.str charmm36-j ul2022.ff python3: can't open file '/home/tomcat/cgenff_charmm2gmx_py3_nx2.py': [Errno 2] No such file or directory ul2022.ff: command not found (.venv) tomcat@LAPTOP-45V3UM01:~ ls
cuda-repo-wsl-ubuntu-12-6-local_12.6.3-1_amd64.deb fftw-3.3.10.tar.gz:Zone.Identifier simgupta5with3hqd
fftw-3.3.10 gromacs-2024.4
fftw-3.3.10.tar.gz gromacs-2024.4.tar.gz
(.venv) tomcat@LAPTOP-45V3UM01:~ cd simgupta5with3hqd/ (.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd ls
3hqd.pdb charmm36-jul2022.ff jz4_fix.str
3hqd_clean.pdb charmm36-jul2022.ff.tgz posre.itp
3hqd_processed.gro charmm36-jul2022.ff.tgz:Zone.Identifier sort_mol2_bonds.pl
JZ4.mol2 jz4.pdb topol.top
cgenff_charmm2gmx_py3_nx2.py jz4.pdb:Zone.Identifier
cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier jz4_fix.mol2
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ python3 cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_fix.mol2 jz4_fix.str charmm36-jul2022.ff
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:62: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:69: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:132: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:143: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:168: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:185: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:581: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:585: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:606: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:622: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:646: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:869: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:896: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
Traceback (most recent call last):
File “/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py”, line 54, in
import networkx as nx
ModuleNotFoundError: No module named ‘networkx’
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ sudo apt install networkx==2.3
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
E: Unable to locate package networkx=
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ python3 cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_fix.mol2 jz4_fix.str charmm36-jul2022.ff
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:62: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:69: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:132: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:143: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:168: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:185: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:581: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:585: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:606: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:622: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:646: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:869: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:896: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
Traceback (most recent call last):
File “/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py”, line 54, in
import networkx as nx
ModuleNotFoundError: No module named ‘networkx’
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ pip install networkx==2.3
Collecting networkx==2.3
Downloading networkx-2.3.zip (1.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 5.6 MB/s eta 0:00:00
Installing build dependencies … done
Getting requirements to build wheel … done
Preparing metadata (pyproject.toml) … done
Collecting decorator>=4.3.0 (from networkx==2.3)
Downloading decorator-5.1.1-py3-none-any.whl.metadata (4.0 kB)
Downloading decorator-5.1.1-py3-none-any.whl (9.1 kB)
Building wheels for collected packages: networkx
Building wheel for networkx (pyproject.toml) … done
Created wheel for networkx: filename=networkx-2.3-py2.py3-none-any.whl size=1555999 sha256=9eaef8ff30f56d12de0b940211c168bec29c7882984cf94c30e1effc2167cf19
Stored in directory: /home/tomcat/.cache/pip/wheels/3e/05/56/d671cde9ea7bef2c76107bcb5e91b8c02040fde6c673db3aff
Successfully built networkx
Installing collected packages: decorator, networkx
Successfully installed decorator-5.1.1 networkx-2.3
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ ls
3hqd.pdb charmm36-jul2022.ff jz4_fix.str
3hqd_clean.pdb charmm36-jul2022.ff.tgz posre.itp
3hqd_processed.gro charmm36-jul2022.ff.tgz:Zone.Identifier sort_mol2_bonds.pl
JZ4.mol2 jz4.pdb topol.top
cgenff_charmm2gmx_py3_nx2.py jz4.pdb:Zone.Identifier
cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier jz4_fix.mol2
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ python3 cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_fix.mol2 jz4_fix.str charmm36-jul2022.ff
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:62: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:69: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:132: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:143: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:168: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:185: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:581: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:585: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:606: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:622: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:646: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:869: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:896: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
Traceback (most recent call last):
File “/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py”, line 54, in
import networkx as nx
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/init.py”, line 114, in
import networkx.generators
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/generators/init.py”, line 14, in
from networkx.generators.intersection import *
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/generators/intersection.py”, line 13, in
from networkx.algorithms import bipartite
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/algorithms/init.py”, line 16, in
from networkx.algorithms.dag import *
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/algorithms/dag.py”, line 23, in
from fractions import gcd
ImportError: cannot import name ‘gcd’ from ‘fractions’ (/usr/lib/python3.12/fractions.py)
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ gmx --version
:-) GROMACS - gmx, 2024.4 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/tomcat/simgupta5with3hqd
Command line:
gmx --version

GROMACS version: 2024.4
Precision: mixed
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 128)
GPU support: CUDA
NBNxM GPU setup: super-cluster 2x2x2 / cluster 8
SIMD instructions: AVX2_256
CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2_128
GPU FFT library: cuFFT
Multi-GPU FFT: none
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: disabled
Tracing support: disabled
C compiler: /usr/bin/cc GNU 13.2.0
C compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -O3 -DNDEBUG
C++ compiler: /usr/bin/c++ GNU 13.2.0
C++ compiler flags: -fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG
BLAS library: Internal
LAPACK library: Internal
CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2024 NVIDIA Corporation;Built on Tue_Oct_29_23:50:19_PDT_2024;Cuda compilation tools, release 12.6, V12.6.85;Build cuda_12.6.r12.6/compiler.35059454_0
CUDA compiler flags:-std=c++17;–generate-code=arch=compute_50,code=sm_50;–generate-code=arch=compute_52,code=sm_52;–generate-code=arch=compute_60,code=sm_60;–generate-code=arch=compute_61,code=sm_61;–generate-code=arch=compute_70,code=sm_70;–generate-code=arch=compute_75,code=sm_75;–generate-code=arch=compute_80,code=sm_80;–generate-code=arch=compute_86,code=sm_86;–generate-code=arch=compute_89,code=sm_89;–generate-code=arch=compute_90,code=sm_90;-Wno-deprecated-gpu-targets;–generate-code=arch=compute_53,code=sm_53;–generate-code=arch=compute_80,code=sm_80;-use_fast_math;-Xptxas;-warn-double-usage;-Xptxas;-Werror;-D_FORCE_INLINES;-Xcompiler;-fopenmp;-fexcess-precision=fast -funroll-all-loops -mavx2 -mfma -Wno-missing-field-initializers -Wno-cast-function-type-strict SHELL:-fopenmp -O3 -DNDEBUG
CUDA driver: 12.50
CUDA runtime: 12.60

(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ ls
3hqd.pdb charmm36-jul2022.ff jz4_fix.str
3hqd_clean.pdb charmm36-jul2022.ff.tgz posre.itp
3hqd_processed.gro charmm36-jul2022.ff.tgz:Zone.Identifier sort_mol2_bonds.pl
JZ4.mol2 jz4.pdb topol.top
cgenff_charmm2gmx_py3_nx2.py jz4.pdb:Zone.Identifier
cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier jz4_fix.mol2
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$ python3 cgenff_charmm2gmx_py3_nx2.py JZ4 jz4_fix.mol2 jz4_fix.str ch
armm36-jul2022.ff
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:62: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:69: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:132: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:143: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:168: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:185: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:581: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:585: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:606: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:622: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:646: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:869: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py:896: SyntaxWarning: invalid escape sequence ‘\s’
entry = re.split(‘\s+’, line.lstrip())
Traceback (most recent call last):
File “/home/tomcat/simgupta5with3hqd/cgenff_charmm2gmx_py3_nx2.py”, line 54, in
import networkx as nx
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/init.py”, line 114, in
import networkx.generators
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/generators/init.py”, line 14, in
from networkx.generators.intersection import *
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/generators/intersection.py”, line 13, in
from networkx.algorithms import bipartite
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/algorithms/init.py”, line 16, in
from networkx.algorithms.dag import *
File “/home/tomcat/.venv/lib/python3.12/site-packages/networkx/algorithms/dag.py”, line 23, in
from fractions import gcd
ImportError: cannot import name ‘gcd’ from ‘fractions’ (/usr/lib/python3.12/fractions.py)
(.venv) tomcat@LAPTOP-45V3UM01:~/simgupta5with3hqd$