AMBER Archive (2008)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu Nov 20 2008 - 07:36:48 CST


On Thu, Nov 20, 2008, Alan wrote:

> 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*
>

??? There is no atom type "ng" in gaff, and I don't see any entries in
gaff.dat that refer to "ng". Could it be that you are looking at an earlier
version of gaff.dat? Bugfix.5 should have removed entries related to "ng".

...dac

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