[gmx-users] Fatal error
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
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?
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