On Tue, Mar 20, 2012 at 1:56 AM, Souvik Sur <souviksur.hotmail.com> wrote:
>
> Hello Sir
> But it generated so many pdb files, suppose if I need five from out of
> 2500 frames, then what will be the script.Please let me know.
>
Only trajin the frames that you wish to print out as PDB files (you can
trajin the same trajectory multiple times in order to pull out 5 random
frames).
Optionally, I think cpptraj has the ability to specify which frames you
want to trajout on the trajout line. This would be described in the
manual. I'm not sure if the cpptraj version from AmberTools 1.5 has that
ability or not (but it will definitely be present in the next version).
In any case, the workaround would be to use my first tip.
HTH,
Jason
> regards,
> Souvik Sur
> Ph. D. Student
> Department Of Chemistry
> University Of Delhi
> India
>
>
> > Date: Mon, 19 Mar 2012 11:17:12 -0400
> > From: jason.swails.gmail.com
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] To generate more than one structure using ptraj
> >
> > On Mon, Mar 19, 2012 at 9:36 AM, Souvik Sur <souviksur.hotmail.com>
> wrote:
> >
> > >
> > > Hello
> > > Can you please suggest me how can I generate more than one structure
> (.pdb
> > > files) from ptraj using my .mdcrd files of simulation.Please help me
> > > regarding it.
> > > regards,
> > >
> >
> > Just specify you want a PDB file on the trajout line:
> >
> > trajout my_file.pdb pdb
> >
> > This will create a separate PDB file for each frame it has stored (it
> will
> > be numbered, i.e. my_file.pdb.0, my_file.pdb.1, etc.).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 20 2012 - 10:30:04 PDT
