[gmx-users] Fatal error
mark.j.abraham at gmail.com
Tue Jul 31 19:49:04 CEST 2018
Why does your final residue, that SER, have only one atom? Is there an
explanation perhaps in the rest of the PDB file?
On Tue, Jul 31, 2018 at 4:15 PM Mohammad Goodarzi <
mohammad.godarzi at gmail.com> wrote:
> 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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