How to fix this problem?
Fatal error: Residue 3 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.
For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/
I think you the problem of you may be you do not delet the ligand when you generate the itp file of protein. you can
1. copy the ligand coordinate from pdb file of protein to a new file and then delet it from protein pdb
2.generate the itp of protein (the AMBER14SB force field is recommended )
3.generate the itp file of ligands (GAFF force field) via acpype
4.copy the gro file (you can use VMD software for formation conversation) to the end of protein gro
5. edit top file of complex
6. run the simulation
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