GROMACS version:
GROMACS modification: Yes/No
Here post your question : Getting following error while building ligand topology.
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 Index of /ubuntu jammy-security InRelease
Hit:3 Index of /ubuntu jammy InRelease
Hit:4 Index of /ubuntu jammy-updates InRelease
Hit:5 Index of /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:~# sudo apt install opnbabel
Reading package lists… Done
Building dependency tree… Done
Reading state information… Done
E: Unable to locate package opnbabel
root@LAPTOP-45V3UM01:~# pip install networkx==2.3
Requirement already satisfied: networkx==2.3 in /usr/local/lib/python3.10/dist-packages (2.3)
Requirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.10/dist-packages (from networkx==2.3) (5.1.1)
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: 12. Virtual Environments and Packages — Python 3.13.0 documentation
root@LAPTOP-45V3UM01:~# ls
Python-3.5.0 charmm36-jul2022.ff jz4.mol2
Python-3.5.0.tgz charmm36-jul2022.ff.tgz jz4_fix.mol2
anand1 charmm36-jul2022.ff.tgz:Zone.Identifier wget-log
anand2 cuda-repo-ubuntu2204-12-6-local_12.6.3-560.35.05-1_amd64.deb
cgenff_charmm2gmx_py3_nx2.py cuda-repo-wsl-ubuntu-12-6-local_12.6.3-1_amd64.deb
root@LAPTOP-45V3UM01:~# cd …
root@LAPTOP-45V3UM01:/# pwd
/
root@LAPTOP-45V3UM01:/# cd home/
root@LAPTOP-45V3UM01:/home# ls
anand1
root@LAPTOP-45V3UM01:/home# cd anand1/
root@LAPTOP-45V3UM01:/home/anand1# ls
3hqdwithGupta5 gromacs-2024.4
fftw-3.3.10 gromacs-2024.4.tar.gz
fftw-3.3.10.tar.gz gromacs-2024.4.tar.gz:Zone.Identifier
fftw-3.3.10.tar.gz:Zone.Identifier gromacs-2024.4.tar.gz:Zone.Identifier:Zone.Identifier
fftw-3.3.10.tar.gz:Zone.Identifier:Zone.Identifier openbabel-openbabel-2-4-0
root@LAPTOP-45V3UM01:/home/anand1# cd 3hqdwithGupta5/
root@LAPTOP-45V3UM01:/home/anand1/3hqdwithGupta5# ls
3hqd.pdb
3hqd.pdb:Zone.Identifier
3hqd_clean.pdb
3hqd_clean.pdb:Zone.Identifier
3hqd_processed.gro
3hqd_processed.gro:Zone.Identifier
‘New Microsoft Word Document.docx’
‘New Microsoft Word Document.docx:Zone.Identifier’
cgenff_charmm2gmx_py3_nx2.py
cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier
cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier:Zone.Identifier
charmm36-jul2022.ff
charmm36-jul2022.ff.tgz
charmm36-jul2022.ff.tgz:Zone.Identifier
charmm36-jul2022.ff.tgz:Zone.Identifier:Zone.Identifier
jz4.pdb
jz4.pdb:Zone.Identifier
jz4_fix.mol2
jz4_fix.mol2:Zone.Identifier
jz4_fix.str
jz4_fix.str:Zone.Identifier
posre.itp
posre.itp:Zone.Identifier
sort_mol2_bonds.pl.txt
sort_mol2_bonds.pl.txt:Zone.Identifier
topol.top
topol.top:Zone.Identifier
tutorial-env
‘~$w Microsoft Word Document.docx’
‘~$w Microsoft Word Document.docx:Zone.Identifier’
root@LAPTOP-45V3UM01:/home/anand1/3hqdwithGupta5# cd tutorial-env/
root@LAPTOP-45V3UM01:/home/anand1/3hqdwithGupta5/tutorial-env# source tutorial-env/bin/activate
-bash: tutorial-env/bin/activate: No such file or directory
root@LAPTOP-45V3UM01:/home/anand1/3hqdwithGupta5/tutorial-env# cd …
root@LAPTOP-45V3UM01:/home/anand1/3hqdwithGupta5# cd …
root@LAPTOP-45V3UM01:/home/anand1# cd …
root@LAPTOP-45V3UM01:/home# cd …
root@LAPTOP-45V3UM01:/# cd …
root@LAPTOP-45V3UM01:/# source /usr/local/gromacs/bin/GMXRC
root@LAPTOP-45V3UM01:/# gmx --version
:-) GROMACS - gmx, 2024.4 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /
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:/# gmx
:-) GROMACS - gmx, 2024.4 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /
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: “gmx fellowship-writing -g grant_name -s protein_structure_involved -o output -m method_used -p list_of_pi” (Tanadet Pipatpolkai, while discussing new features for GROMACS)
root@LAPTOP-45V3UM01:/# cd home
root@LAPTOP-45V3UM01:/home# ls
anand1
root@LAPTOP-45V3UM01:/home# cd anand1/
root@LAPTOP-45V3UM01:/home/anand1# ls
3hqdwithGupta5 gromacs-2024.4
fftw-3.3.10 gromacs-2024.4.tar.gz
fftw-3.3.10.tar.gz gromacs-2024.4.tar.gz:Zone.Identifier
fftw-3.3.10.tar.gz:Zone.Identifier gromacs-2024.4.tar.gz:Zone.Identifier:Zone.Identifier
fftw-3.3.10.tar.gz:Zone.Identifier:Zone.Identifier openbabel-openbabel-2-4-0
root@LAPTOP-45V3UM01:/home/anand1# cd 3hqdwithGupta5/
root@LAPTOP-45V3UM01:/home/anand1/3hqdwithGupta5# ls
3hqd.pdb
3hqd.pdb:Zone.Identifier
3hqd_clean.pdb
3hqd_clean.pdb:Zone.Identifier
3hqd_processed.gro
3hqd_processed.gro:Zone.Identifier
‘New Microsoft Word Document.docx’
‘New Microsoft Word Document.docx:Zone.Identifier’
cgenff_charmm2gmx_py3_nx2.py
cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier
cgenff_charmm2gmx_py3_nx2.py:Zone.Identifier:Zone.Identifier
charmm36-jul2022.ff
charmm36-jul2022.ff.tgz
charmm36-jul2022.ff.tgz:Zone.Identifier
charmm36-jul2022.ff.tgz:Zone.Identifier:Zone.Identifier
jz4.pdb
jz4.pdb:Zone.Identifier
jz4_fix.mol2
jz4_fix.mol2:Zone.Identifier
jz4_fix.str
jz4_fix.str:Zone.Identifier
posre.itp
posre.itp:Zone.Identifier
sort_mol2_bonds.pl.txt
sort_mol2_bonds.pl.txt:Zone.Identifier
topol.top
topol.top:Zone.Identifier
tutorial-env
‘~$w Microsoft Word Document.docx’
‘~$w Microsoft Word Document.docx:Zone.Identifier’
root@LAPTOP-45V3UM01:/home/anand1/3hqdwithGupta5# python3 cgenff_charmm2gmx.py3 JZ4 jz4_fix.mol2 jz4_fix.str c
harmm36-jul2022.ff
python3: can’t open file ‘cgenff_charmm2gmx.py3’: [Errno 2] No such file or directory
root@LAPTOP-45V3UM01:/home/anand1/3hqdwithGupta5#