GROMACS version: gmx grompp, version 2023-openSUSE
GROMACS modification: Yes/No
Hi all,
I am working on my covalent ligand-protein model (Cys-ligand) and adding Cys-ligand as a new residue to FF (charmm36-jul2022.ff). I got an issue using
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117432 of the 167910 1-4 parameter combinations
ERROR 1 [file topol.top, line 950]:
Atomtype ns not found
Program: gmx grompp, version 2023-openSUSE
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1436)
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Line 950 in topol.top file is corresponding to N atom of Cys that makes peptide bond with neighboring ASN residue in protein. I have used for acpype for parametrization of Cys-lig model and modified aminoacids.rtp, aminoacids.hdb and aminoacids.rtp files accordingly.
I appreciate any help/suggestion fixing issue.
Bests
Zahra