[gmx-users] Fatal error

[Mark Abraham]

Hi,

Why does your final residue, that SER, have only one atom? Is there an
explanation perhaps in the rest of the PDB file?

Mark

On Tue, Jul 31, 2018 at 4:15 PM Mohammad Goodarzi <
mohammad.godarzi at gmail.com> wrote:

> Hello,
>
> 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
> here
> https://www.dropbox.com/sh/4r9jhrwmgfmodh6/AAB8TJYep7NvO7w7APJY0PlAa?dl=0
>
> 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
> Mohammad
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