[gmx-users] Fatal error

Mohammad Goodarzi mohammad.godarzi at gmail.com
Tue Jul 31 17:14:43 CEST 2018


I am trying to run the following command but I always get error
I download my PDB from https://www.rcsb.org/structure/2J3S
Then I remove water, ligand and keep only chain A by pymol
Then I mutate the site that I am interested in and you can find the new PDB

then I run the following

gmx pdb2gmx -f A2236.pdb -o conf.pdb

No matter which force field I use, I get an error like

Fatal error:

Residue 271 named SER of a molecule in the input file was mapped

to an entry in the topology database, but the atom CA used in

that entry is not found in the input file. Perhaps your atom

and/or residue naming needs to be fixed.

can anyone help me to fix the problem?
Many thanks

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