VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Jul 15 2009 - 17:32:07 CDT

Hi Thomas,

2009/7/15 Thomas Evangelidis <te8624_at_mbg.duth.gr>:
> 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.

Cheers,
Leo

> thanks in advance,
> Tom
>
> 

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