VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 10 2009 - 10:56:08 CDT

Hi,
  You can easily add additional selection keywords to complete the
selection you're aiming for, e.g. "protein and resname FOO" or something
like that. These topics are covered in the VMD tutorials, but the full
list of atom selection keywords is provided in the VMD User's Guide.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 08, 2009 at 03:47:43PM -0700, Sujata Sovani wrote:
> Hi VMD USers,
>
> I am new and following the NAMD tutorial for ubq.
> I have a protein with ATP and acetylated N-term.
>
> When I do
> set xyz [atomselect top protein]
> $xyz writepdb xyznew.pdb
>
> ATP gets deleted (and so does ACE which is fine) but I need ATP.
> When I do
>
> set xyz [atomselect top all]
> $xyz writepdb xyznew.pdb
> ACE and ATP stay and then when I convert it to PSF file, I get a fatal
> error due to ACE. I can delete ACE from xyznew.pdb and proceed but if I do
> this something weird happens to my ATP and I get repeated errors when I
> run NAMD.
>
> I want to know - is there a way to keep the hetatom ATP and remove ACE
> right at the first stage of writing pdb from the original pdb - in the
> atomselect command or thereafter?
>
> Thanks. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078