VMD-L Mailing List

From: Ricardo Soares (rsoares_at_fcfrp.usp.br)
Date: Tue Nov 29 2011 - 13:25:16 CST

Hello,

thanks you all for your reply.
I'm not sure it could be directly done, to use the beta or occupancy fields to
create a selection for Gromacs. Plus, the system (protein+ions+water) has the
beta column filled with zeros.

Anyway, I could successfully select the atoms with its original numbering with
the use of pdbcat and awk.

Thanks for your help!

Ricardo.

On Tue, 29 Nov 2011 10:25:22 -0600, John Stone wrote
> 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