AMBER Archive (2004)

Subject: Re: AMBER: trajectory file

From: Andy Purkiss (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Mon Mar 29 2004 - 10:54:24 CST

Dear Joseph,

You input file should look like this. The ; tells carnal that this is
the end of the stream and you can use as many lines as you want.

FILES_IN
  PARM p1 p1.top;
  STREAM s1 a.pdb
            b.pdb
            c.pdb
            d.pdb
            e.pdb
            f.pdb;
FILES_OUT
  COORD c1 abcdef.crd;
DECLARE
  COORD c1 s1 s2;
END

Andy Purkiss

On Mon, 2004-03-29 at 18:16, Joseph Nachman wrote:
> Since I have about 50 PDB files, it makes the statement STREAM longer than
> the 80 characters Carnal accepts. I wonder if something like that would
> work:
>
> FILES_IN
> PARM p1 p1.top;
> STREAM s1 a.pdb b.pdb c.pdb;
> STREAM s2 d.pdb e.pdb f.pdb;
> FILES_OUT
> COORD c1 abcdef.crd;
> DECLARE
> COORD c1 s1 s2;
> END
>
> Thanks,
>
> Joseph
>
> On Tue, 16 Mar 2004, Bill Ross wrote:
>
> > > I'd like to make pseudo-trajectory file from a number of pdb or
> > > coordinate/restart files. Is there a way to do that by using either Ptraj
> > > or Carnal?
> >
> > In carnal, put your pdb files in a STREAM and point it at
> > a COORD (default is mdcrd format). Adapting the simple
> > initial example in the carnal manual:
> >
> > FILES_IN
> > PARM p1 ketop;
> > STREAM s1 a.pdb b.pdb c.pdb;
> > FILES_OUT
> > COORD c1 abc.crd;
> > DECLARE
> > OUTPUT
> > COORD c1 s1;
> > END
> >
> > Bill
> > -----------------------------------------------------------------------
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> > 

-- 
Growing old is inevitable, growing up is optional
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|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail   a.purkiss_at_mail.cryst.bbk.ac.uk                   |
|      Phone 020 7631 6869 (Work) or 020 7237 1165 (Home)             |
|                     Mobile: 07763 490 360                           |
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