VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Sep 05 2007 - 11:05:12 CDT

Hi,

I have coordinates of the choline headgroup of a PC lipid from a crystal
structure, and am trying to use psfgen to guess the coordinates of the rest
of the lipid molecule

The guessing goes very well, except that for some reason, two of the
carbonyl atoms (one in each alkyl chain) are guessed to be at the origin
(0,0,0); quite far away from the rest of the molecule. Can anyone tell me
what I am doing wrong ?

Here is the script being used. The file pop1.pdb has the coordinates of
choline.

############
resetpsf
package require psfgen
topology top-combined.rtf

segment POP1 {
first none
last none
pdb pop1.pdb }
coordpdb pop1.pdb POP1

guesscoord
regenerate angles dihedrals

writepdb popc-only.pdb
writepsf popc-only.psf
############

Thank you

-Maria 

-- 
Maria G.
Technical University of Denmark
Copenhagen