# Getting error while generating ligand topology **URL:** \ **Category:** User discussions\ **Created:** [December 1, 2024, 3:43am UTC](https://gromacs.bioexcel.eu/t/getting-error-while-generating-ligand-topology/10669 "2024-12-01T03:43:58Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![Anandsingpatil1983](https://avatars.discourse-cdn.com/v4/letter/a/ccd318/32.png) [@Anandsingpatil1983](https://gromacs.bioexcel.eu/u/Anandsingpatil1983)\ **Post date:** [December 1, 2024, 3:43am UTC](https://gromacs.bioexcel.eu/t/getting-error-while-generating-ligand-topology/10669/1 "2024-12-01T03:43:58Z")
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](http://security.ubuntu.com/ubuntu) jammy-security InRelease Hit:3 [Index of /ubuntu](http://archive.ubuntu.com/ubuntu) jammy InRelease Hit:4 [Index of /ubuntu](http://archive.ubuntu.com/ubuntu) jammy-updates InRelease Hit:5 [Index of /ubuntu](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:~# 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](https://pip.pypa.io/warnings/venv) 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#