AMBER Archive (2002)

Subject: Re: topology file generation

From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Mon May 06 2002 - 07:24:30 CDT

Thanks very much for the information. I earlier tried tleap < ipfile, and
it cribbed saying something that I vaguely remember as rdirection was not
enabled or some silimar thing. Today again with some suspicion I rechecked
and found that there is a '-f' option. Apologies for everyone...

-Sanjeev

On Mon, 6 May 2002, Andreas Svrcek-Seiler wrote:

Hi,
> Hello,
> I would like to automate generation of topology file for a large
> number of PDBs.
...
Provided your pdbs are 'clean', the easiest way to do this
that comes to my mind is using NAB:

the following NAB 'program' reads in a pdb file
and writes out a prmtop file ( named 'prmtop'):