From: Leonardo Trabuco (
Date: Wed Jul 15 2009 - 17:32:07 CDT

Hi Thomas,

2009/7/15 Thomas Evangelidis <>:
> simple question:
> I wan to parse some pdb files and keel only the specified ligand/s. e.g.
> set protMol [mol new 1BQG.pdb]
> animate write pdb "PDB/1bqg.pdb" sel [atomselect $protMol "protein or
> resname RMN SMN"] $protMol
> mol delete $protMol
> However the ligands RMN and SMN are converted to ATOMS which encumbers
> further analysis with other programs. How can I avoid that?

Simple answer:

1) write a script to replace "ATOM" with "HETATM" after VMD wrote the file;

2) or modify the molfile plugin pdbplugin.c do what what you want.


> thanks in advance,
> Tom

Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign