Re: ambpdb in AMBER7

From: David Case <>
Date: Wed 22 May 2002 14:09:32 -0700

On Wed, May 22, 2002, Matthew Lee wrote:

> I am interested in getting Brookhaven PDB format from my restart file.
> According to the AMBER7 documentation, this should be possible with
> the -aatm flag of ambpdb.

No, Brookhaven PDB format is the default. Setting "-aatm" asks for
Amber atom names, which are *not* those used by Brookhaven. Using this
flag is rarely necessary, since Amber reads in Brookhaven atom names and
converts them; but there may be programs out there which would benefit
from this flag.

> However, it seems that the -aatm flag wipes
> out atom types altogether.

You are correct. I have posted a bugfix (bugfix.14) on the Amber Web site.

Thanks for reporting this problem.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Wed May 22 2002 - 14:09:32 PDT
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