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