Please help me to solve this step in writing ligand topology

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
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 noble-security InRelease [126 kB] Hit:3 https://ppa.launchpadcontent.net/deadsnakes/ppa/ubuntu noble InRelease Get:4 http://security.ubuntu.com/ubuntu noble-security/main amd64 Packages [498 kB] Hit:5 http://archive.ubuntu.com/ubuntu noble InRelease Get:6 http://archive.ubuntu.com/ubuntu noble-updates InRelease [126 kB] Get:7 http://security.ubuntu.com/ubuntu noble-security/universe amd64 Packages [562 kB] Hit:8 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 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$ 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$