[gmx-users] problems with chain IDs for huge complex

[Tomek Wlodarski]

As far as I remember in pdb format you can only use one character for chain
id.



On Mon, Nov 18, 2013 at 7:05 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> How about naming your chains AA-AZ then BA-BZ? You probably need to change
> the chain names in the original structures rather than just renaming the
> files.
>
> > Hi,
> >
> > I am preparing simulation of the ribosome and because of it size I am
> > force
> > to use A-Z and a-z to name all chains...
> > With pdb2gmx it is not a problem but with grompp I am ending up with this
> > error (gromacs 4.6.3):
> >
> > Fatal error:
> > moleculetype Protein_chain_b is redefined
> >
> > I figured out that for grompp Protein_chain_b and Protein_chain_B are the
> > same entry - and hence error...
> > I changed the name of files in this fashion:
> > Protein_chain_b -> Protein_chain_bb etc
> > And now grompp was able to read them but it found out that there is
> > different number of atoms between top and gro file..
> > Any ideas or suggestions?
> > Thanks.
> > Best
> >
> > tomek
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