AMBER Archive (2009)

Subject: Re: [AMBER] gaff.dat questions

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Sep 09 2009 - 09:16:23 CDT

On Wed, Sep 09, 2009, gilbert_at_bluemarble.net wrote:
> I found a duplicate entry for the cd-cd bond in gaff.dat
>
> 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 was corrected in bugfix.5. Be sure to apply all the bugfixes, since
there are some significant ones, especially in AmberTools.
>
> Also the torsion data has a large number of entries with a barrier
> height of 0.0. Are these just place holders to be updated at some
> future time or does the amber prep code not zero out all torsions for
> which there are no data. Since these torsions don't contribute to the
> rotational barrier why include them in the parameter file.

Junmei know the "real answer" here, but I think he started with a template
file of all zeroes, then systematically replaced the zeroes with non-zero
values as he parameterized various torsions. I'm not sure whether gaff
version 2 will have fewer zeroes there or not. They could be eliminated.

...regards...dac

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