VMD-L Mailing List

From: Ricardo Soares (rsoares_at_fcfrp.usp.br)
Date: Tue Nov 29 2011 - 18:58:56 CST

Dear Mr. Lai,

thanks for your help.
It was something like this that I was looking for. The key step for me was
"[$sel get serial]". That worked like a charm, and the selection comfirmed my
previous efforts.

Thanks again,

Ricardo.

On Tue, 29 Nov 2011 17:22:35 -0600, Peter C. Lai wrote
> 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
> >
>
> --
> ==================================================================
> Peter C. Lai | University of Alabama-Birmingham
> Programmer/Analyst | KAUL 752A
> Genetics, Div. of Research | 705 South 20th Street
> pcl_at_uab.edu | Birmingham AL 35294-4461
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