Hi -
Thanks for the tip.
I tried the example you gave me, and I got the error message:
input stdin
> FILES_IN
> PARM p1 1spshm.top;
Reading parm file (1spshm.top)
parm: opening 1spshm.top
1spshm.top title:
> STREAM s1 1000/minhm_1000_51.pdb 1000/minhm_1000_1.pdb;
Using default parm (1spshm.top) for STREAM s1
stream: opening 1000/minhm_1000_1.pdb
Error: 1000/minhm_1000_1.pdb: full pdb format not supported
Only ATOM records in amber order allowed
The PDB were obtaine from restart files using ambpdb.
Here is my input:
FILES_IN
PARM p1 1spshm.top;
STREAM s1 1000/minhm_1000_51.pdb 1000/minhm_1000_1.pdb;
FILES_OUT
COORD c1 minhm_1000.crd
DECLARE
OUTPUT
COORD c1 s1;
END
I wonder if instead of using PDB files, I can use the restart files.
Thaanks,
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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--
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Joseph Nachman Department of Biochemistry
nachman.hera.med.utoronto.ca University of Toronto
Medical Sciences Building
tel: +1 416 978-5510 Toronto, Ontario M5S 1A8
fax: +1 416 978-8548 Canada
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Received on Tue Mar 23 2004 - 22:53:00 PST
