VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 29 2011 - 10:25:22 CST

Hi,
  Can you use the beta or occupancy fields to create a selection for Gromacs?
This is how NAMD reads PDB files to identify which subset of atoms are
selected. In that case, one just sets the beta/occupancy fields in VMD,
writes a new PDB file, and then NAMD/Gromacs/other tool reads the PDB file
and interprets those fields to determine which atoms are selected.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 29, 2011 at 08:47:33AM -0300, Ricardo Soares wrote:
> Dear VMD users,
>
> I'd like to save an specific selection as coordinates in a PDB file, so I can
> make an GROMACS index file out of it. For this, I need that VMD maintains the
> original atom numbering, so I can identify the selected atoms. "Writepdb"
> always reissues a new numbering, starting from 1, which scrambles everything.
>
> Any ideas or known scripts?
>
> Thanks in advance, 

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