VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Sat Feb 07 2009 - 11:02:30 CST

Dear VMD users,

I have 3 separate .pdb files, the receptor, the co-crystalized
inhibitor, and a potential inhibitor. I am trying to create one file
(it doesn't matter if it will be .pdb or another readable format) that
will contain all these 3 molecules in order to be able to measure
Hbonds between them. However the bond information in ligand .pdb files
(lines starting with "CONECT") pose a problem, as the atom indices
between the 2 ligands clash. Moreover when I try to save the ligand
coordinates as .pdb files no information about bonds is saved.
The reason I'm asking all these is because I'm trying to render the
receptor as NewCartoon and that drawing method work when loading the
receptor .pdb but not when loading the complex with the 2 ligands.

any advice would be deeply appreciated,

Tom