VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jul 12 2006 - 11:24:34 CDT

Why not use the chain or segment identifiers to break up your long
list of residues? i.e. chain A: residues 1 - 5000, chain B: residues
1 - 5000, etc.

On Jul 12, 2006, at 10:56 AM, Vlad Cojocaru wrote:

> Dear VMD developers,
>
> Is there a way to change the pdb output from vmd such as to allow
> residue numbers greater than 9999 and to eliminate the X chain
> identifier?
>
> I am trying to save a number of pdb files by selecting "water within 5
> of protein" and the pdb output has strange residue numbers such as
> X34ef5. The problem with these pdb files is that whenever I try to
> load
> them in other programs, the residues are not recognized anymore.
> This is
> especially painful if I want to use the created pdb files back into
> the
> Leap program from Amber ...
>
> Best wishes
> vlad
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
>