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

[jkrieger at mrc-lmb.cam.ac.uk]

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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