VMD-L Mailing List

From: satya kumar (mail2mvskumar_at_gmail.com)
Date: Mon Jul 09 2012 - 15:35:44 CDT

Please ignore my previous question. Thanks for all your help.

With Regards,
Satya.

On Mon, Jul 9, 2012 at 12:31 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> 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
>