Hi. 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). Questions: 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
