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

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

Maybe the answer is to not worry about chain identifiers until analysis
stages - you could probably just call everything chain A at the start. You
can then create an index entry for each chain. See
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains

> 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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