AMBER Archive (2008)

Subject: Re: AMBER: Duplicate entries with different parameters in gaff.dat from AmberTools 1.2 (resend)

From: Alan (alanwilter_at_gmail.com)
Date: Thu Nov 20 2008 - 05:48:56 CST

Hello, I have some doubts here.
So I compared gaff.dat (pre-patch) with new gaff.dat and found some unusual
diffs:

c1-ng 465.7 1.353 SOURCE3 3 0.0025 0.0027

is not in new gaff.dat. But I guess I can understand it since there's no
atom type 'ng' in neither old or new gaff.dat. Or 'ng' is missing too?

The same for:

c1-ng-ng 51.9 179.97 HF/6-31G*

Many thanks in advance,
Alan

On Wed, Nov 19, 2008 at 14:35, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Tue, Nov 18, 2008, John Chodera wrote:
> >
> > I just noticed that the copy of gaff.dat (the GAFF parameter
> > definition file) appearing in AmberTools 1.2 contains repeated
> > entries, but with these entries specifying different parameters. For
> > example, in the bond section:
> >
> > cd-cd 418.3 1.429 SOURCE1 740 0.0058 0.0069
> > cd-cd 504.0 1.371 SOURCE3 523 same as cc-cd
>
> This appears to have been caused by Junmei himself, who did not use CVS
> at one point in 2006 in creating an updated gaff.dat file. This lost
> corrections made in CVS revisions 8.1 and 8.2.
>
> I have fixed this in CVS, and posted a bugfix to the web site.
>
> Thanks again to John for pointing this out. Please let us know if still
> find
> problems.
>
> ...dac
>
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-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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