VMD-L Mailing List

From: poker_at_physics.usyd.edu.au
Date: Wed Jun 17 2009 - 02:30:55 CDT

I'm attempting to reconstruct an all-atoms POPG/POPE lipid from its partial
crystallographic coordinates (this lipid is in close association with
protein).
At the moment, I've edited the original pdb file to match atom names and resid's
- but run into problems when psfgen supplies badly guessed hydrogens. s.g. the
poorly guessed atoms from a molecule all cluster to one point that is not {0 0
0}.

I've tried removing the hydrogens and re-running the script, but this doesn't
seem to fix the problem. We're using the charmm27 topology files for POPG and
POPE.

Can anyone advise me on what I could do next? Or is there a program I can use to
quickly manipulate the dihedrals of a theoretical lipid to match the
conformation of my experimental fragment?

thanks,
Poker.