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

[Tomek Wlodarski]

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