[gmx-users] pdb2gmx with more than 9999 residues

Jernej Zidar jernej.zidar at gmail.com
Tue Oct 2 08:16:00 CEST 2012

  I'm trying to import a solvated lipid bilayer
(cholesterol+POPC+water) I generated in CHARMM but I have a problem
with pdb2gmx unwilling to accept the segment containing water
molecules. It does import everything seemingly correctly, yet when one
examines the resulting .gro file, he can see that the system does not
accept more than 9999 residues/segment: residue 10000 becomes 1000 and
so on.

  Now, what can one do ammend the current situation?

  One option would be to import only the lipid part of the system and
then solvate it again in GROMACS, but that path is not really useful
because it doesn't allow to fine tune the amount and location of water
molecules. I tried this option but it doesn't work in my case as
there's a gaping hole between the water layer and the lipids, that
cause the minimization to essentially fail.

  Another option would be to import the lipid and water part
separately but this would again cause problems with atom numbering
when both segments would be combined together.

  Manually editing the PDB file is not an option as the PDB file has
~80.000 lines.

  Any other way?

  I'm using GROMACS 4.5.5 on Ubuntu 12.04 64-bit.

Thanks in advance,

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