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.mail.cryst.bbk.ac.uk |
| Phone 020 7631 6869 (Work) or 020 7237 1165 (Home) |
| Mobile: 07763 490 360 |
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Received on Mon Mar 29 2004 - 18:53:00 PST
