I am running protein-ligand simulation in Gromacs, but when i run grompp command the fatal error shows up saying that, Atomtype CH3 not found.
I am using OPLS ff.
The .GRO and .ITP files of ligand was obtained from PRODRG server.
Define CH3 atom type or change it if it is defined under another name.
Martin Klvana , The atomtype CH3 was defined as you suggested, which was coded differently in complex.gro file. But also the same error occurred, kindly explain.
i don't use Gromacs, but i assume that for the atom type (CH3) to be recognized the only thing that needs to be done is to define the atom type in the force field file.
A google search will be more helpful. The error indicates the atom CH3 is not defined/identified when compiler map the input files with forcefield parameters. If it is a new molecule you need to make sufficient files to include in ff. If it is biomolecules like proteins, your input files are not in standard form as per GROMACS.
PRODRG server are not good enough for parameterization of OPLS>
Dont forget to insert itp file in topology.
@Nikhil, Sir i have added CH3 atoms to the necessary input files, but i am not sure it is correct or not (not sure in which ff file i have to add). And as you mentioned, i have obtained the topology file (.top) and .gro of ligand from PRODRG server. Kindly help.
Follow Justin tutorial on the protein-ligand system. Share your files here, Topol, pdb and itp file you have obtained from the server.
PRODRG produces (bad) topologies for GROMOS force fields. Do not attempt to mix and match force fields - the resulting physical model is completely invalid, even if you manage to hack the force field files to "make it work." Use the LigParGen server for OPLS topologies.
@Nikhil and @Justin, I will try as suggested sir.
@Nikhil, can i share it personally sir, to your email.
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