AMBER Archive (2002)

Subject: Re: ambpdb in AMBER7

From: David Case (case_at_scripps.edu)
Date: Wed May 22 2002 - 16:09:32 CDT

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.

...regards...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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