AMBER Archive (2003)

Subject: Re: AMBER: ambpdb

From: ch cureton (charlie_at_pugh.bip.bham.ac.uk)
Date: Fri Dec 12 2003 - 05:53:17 CST

Lan,
Here is a copy of an analin file that generates multiple pdb files from a
single mdcrd (frames 1, 500 and 1000):

FILES_IN
  PARM p1 prmtop;
  STREAM s1 mdcrd;
FILES_OUT
  COORD c1 filename.pdb PDB;
DECLARE

OUTPUT
  COORD c1 s1 SELECT (1 500 1000);

END

Hope this helps
Charly

On Fri, 12 Dec 2003, L Jin wrote:

> Charly,
> Thank you for reply. How do you specify the frame number of the mdcrd? With
> DECLARE, GROUP? Please write the specific command line. Thank you very much.
>
> Lan
>
>
>
>
> Quoting ch cureton <charlie_at_pugh.bip.bham.ac.uk>:
>
> > Lan,
> > You can get a single or series of pdb files from a mdcrd using Carnal, you
> > use the mdcrd as the input stream and specify the frame number of the
> > mdcrd you want as a pdb in the output coordinate selection.
> > Hope this helps
> > Charly
> >
> > On Fri, 12 Dec 2003, L Jin wrote:
> >
> > > Hi amber users,
> > >
> > > Please is there anyone know how to use ambpdb to get a new pdb file from a
> > mdcrd
> > > file? I can use ambpdb to get pdb from the restrt file, but it is just one
> > pdb
> > > file or one frame. Is it possible to get a series of pdb files with ambpdb?
> > Or
> > > with some other commands or methods. Thank you very much
> > >
> > > Lan
> > >
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