AMBER Archive (2008)

Subject: Re: AMBER: Amber 10 ambpdb bug?

From: Sam Danziger (sam.danziger_at_gmail.com)
Date: Sun May 18 2008 - 22:41:43 CDT

That fixed it. Thank you!

-Sam

On Sat, May 17, 2008 at 9:37 PM, David A. Case <case_at_scripps.edu> wrote:
> On Sat, May 17, 2008, Sam Danziger wrote:
>
>> Specifically, using the same input files as the Amber 8 ambpdb the
>> atoms that were previously called H1,H2,H3 are called 1H,2H,2H.
>>
>> Is this a bug, or is there something important that I'm overlooking?
>
> It certainly is a bug. Change "2H" at line 564 of ambpdb.f to "3H". I'll
> post a bugfix. Thanks for reporting this.
>
> But this just solves a part of the problem, since LEaP also needs to be
> updated. A better workaround for now (aside from manually editing the file
> that ambpdb puts out) is to remove lines 556-565 of ambpdb.f.
>
> As a side note: the pdb has recently updated its atom nomenclature, especially
> for hydrogen atoms: http://remediation.wwpdb.org/downloads.html. The new
> scheme used by pdb is much closer (virtually identical) to the internal Amber
> nomenclature -- Amber has always followed IUPAC standards, and the pdb is only
> now coming up to speed on this.
>
> This means that many of the contortions in codes like ambpdb are no longer
> strictly necessary. But in the short term, things will probalby be more
> confusing, since we will have to deal with both old and new formats. I'll be
> posting soon an updated ambpdb that will output the new pdb atoms names.
>
> ...regards...dac
>
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-- 
Samuel A. Danziger
Dept. of Biomedical Engineering
PhD Candidate
University of California
Irvine, CA 92697
sdanzige_at_uci.edu
(908)246-4502
http://samdanziger.com/

Associated Graduate Students
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Truth Cannot Contradict Truth
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