VMD-L Mailing List

From: Peter C. Lai (pcl_at_uab.edu)
Date: Tue Nov 29 2011 - 17:22:35 CST

Make the selection in the TK Console:

set sel [atomselect molid "the selection you want for index group"]

set atomlist [$sel get serial]

$atomlist will now be a list of all the atoms in the selection.

Copy paste the list into a new section in your ndx file ([MY_SELECTION])

and then you can reference it in grompp or whatever.

On 2011-11-29 01:25:16PM -0600, Ricardo Soares wrote:
> 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
> 

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