From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 09 2012 - 11:31:39 CDT

Hi,
  You would do something like this:

set sel [atomselect top "within 5 of nucleic"]
$sel writepdb selected.pdb
$sel delete

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 09, 2012 at 11:16:58AM -0400, satya kumar wrote:
> Hello,
> Thanks. May be I can save as .pdb file and then convert to .gro file. I
> have used the following command to save the coordinates as .pdb file
> in the console: writepdb sample.pdb, but it wasn't working. Could you
> guide me.
> With Regards,
> Satya.
> On Mon, Jul 9, 2012 at 11:08 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> You can use scripting commands to create an atom selection such as you
> have already used, and then write a PDB or another file format that you
> can convert to a .gro file. The VMD plugins read .gro files but at
> present
> they do no implement writing support.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Mon, Jul 09, 2012 at 09:15:51AM -0400, satya kumar wrote:
> > Firstly thanks a lot for the help. The command "within 5 of
> nucleic"
> > worked and I need to save the coordinate file as a .gro file. Is
> there a
> > way that I can save this file from VMD?
> > With Regards,
> > Satya.
> > On Sat, Jul 7, 2012 at 12:05 AM, Axel Kohlmeyer
> <akohlmey_at_gmail.com>
> > wrote:
> >
> > On Sat, Jul 7, 2012 at 1:34 AM, satya kumar
> <mail2mvskumar_at_gmail.com>
> > wrote:
> > > Hello VMD users,
> > >
> > > I am working on Molecular Dynamics simulations. I have a file
> > sample.gro
> > > that has a box consisting of DNA molecule+water molecules in my
> > system. I
> > > have to choose all the water molecules that are close to the
> dna (with
> > some
> > > cut off distance). Is there a way that VMD selection can handle
> it?
> >
> > yes. the atom selection syntax has a "within <distance> of"
> > as well as an "exwithin <distance> of" keyword and using
> > the "same fragment as" expression selects entire molecules.
> >
> > all you have to do is to combine these with descriptions that
> > match your water and DNA molecules and then you have
> > your custom selections. for details, please have a close look
> > at the examples and documentation of the atom selection
> > syntax in the VMD user's guide.
> >
> > axel.
> > >
> > > Request you to guide me. Thanks for your time.
> > >
> > > With Regards,
> > > Satya.
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > International Centre for Theoretical Physics, Trieste. Italy.
>
> --
> 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

-- 
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