[gmx-users] error using pdb2gmx

[Irem Altan]

Hi,

Thank you for your reply. Should I generate the topology file with the .pdb file with only one copy of the protein, then? I am also a bit unfamiliar with editing topology files. I have looked at the Gromacs manual. Isn’t the system field for defining the title of the system?

Best,
Irem

> On Jan 6, 2016, at 2:52 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
> You don't need to run pdb2gmx to generate copies, just edit the [system]
> field of your topology to match your coordinate file.
> 
> Mark
> 
> On Wed, Jan 6, 2016 at 8:38 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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