AMBER Archive (2004)

Subject: Re: AMBER: trajectory file

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Tue Mar 23 2004 - 16:38:28 CST

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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Joseph Nachman				Department of Biochemistry
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