[gmx-users] error using pdb2gmx

[Mark Abraham]

Sorry, maybe it's [molecules]. Chapter 5 is your best friend ;-)

Mark

On Wed, Jan 6, 2016 at 9:35 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> I have a .pdb file that I generated by creating three more copies of the
> protein according to its P212121 symmetry. I am now trying to run pdb2gmx
> on it, but I get the following error:
>
> Fatal error:
> Residue 111 named CYS 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.
>
> What is weird is that there is no residue 111 that is a cysteine (residue
> 111 is a phenylalanine). I had run MD simulations successfully on a single
> copy of this protein before. pdb2gmx runs without an error when I use the
> old .pdb file. What could be the problem?
>
> Best,
> Irem
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