VMD-L Mailing List

From: Satyavani Vemparala (vani_at_VITAE.CMM.UPENN.EDU)
Date: Mon Feb 16 2004 - 15:18:49 CST

I have a DOPC coordinate file (PDB) in which the residue numbers is
repeating. i.e.,

side chains (OLEO) have residue numbers 1 & 3
the head group (PCGL) has residue number 2

and this repeats for all the lipid molecules (the last entry in every
column has the the information about the lipid number e.g.,:

ATOM 1 C1 OLEO 1 25.238 -18.360 17.677 0.00 0.00 L001
ATOM 139 C1 OLEO 1 -10.888 -25.455 14.071 0.00 0.00 L002

when iam trying to use psfgen to generate psf files, it does that only for
the first lipid molcule and gives errors for all the other lipids:

building segment U1
reading residues from pdb file dopc-h.pdb
duplicate residue key 1
ERROR: failed on residue OLEO from pdb file
duplicate residue key 2
ERROR: failed on residue PCGL from pdb file
duplicate residue key 3

I guess the tedious way is to seperate each segment into a pdb file and
then use psfgen (in which segment info is to be repeated 72 times!)

But i was wondering if there is an easier way out of it.

Thanks
vani