[gmx-users] Problem: pdb2gmx with a more complex system

Jernej Zidar jernej.zidar at gmail.com
Tue Mar 27 03:57:26 CEST 2012

  I'm trying to import a PDB containing the following components to
Gromacs using pdb2gmx:
- polymer (1 molecule composed of 5 residues)
- lipids (cholesterol-37 molecules and sphingomyelin-78 molecules)
- water (2297 molecules)

  The problem I have is that for some strange reason pdb2gmx does not
recognize the lipid part as being composed of 112 molecules, but
rather just as one molecule.
  If I attempt to manually correct this to 112, grompp complains about
the system containing 1345900 atoms (total number of lipid atoms
11954*112 molecules+161 from the polymer bit+6891 from water) instead
of 19006 atoms (161 from the polymer bit, 11954 from the lipids, 6891
from water).

a) Why are the water molecules properly recognized? The only thing I
had to do was to use some sed commands to change the segment name from
"bulk" to SOL and the atomtypes from TIP3 (OH2, H1, H2) to SPC (OW,
HW1, HW2).

b) I used CHARMM to generate the lipid bilayer. The membrane building
process occurs in two stages so the residues in the resulting bilayers
are arranged in this order: cholesterol, sphingomyelin, cholesterol,
sphingomyelin. Could this be the cause?
  Why aren't the lipid residues recognized as separate molecules?

  The lipid molecules are defined as separate molecules in the joined
charmm36cgenff forcefield, where I used the existing lipid molecules
in lipids.rtp as a template to add my own molecules.

  I should emphasize the all the residues/molecules work perfectly
within CHARMM, but then again CHARMM has a different modus operandi.

Thanks in advance for any help,
Jernej Zidar

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