Re: amber-developers: Question concerning wildcards in dihedral definitions.

From: Guanglei Cui <>
Date: Wed, 29 Jun 2005 10:54:43 -0700

I didn't do anything new. I only described what I did to fit the
torsion. Sorry for the confusion. In, the 3-fold term has a
zero pk and it's the only definition for c1-os-p5-o . The original
2-fold term was replaced by this specific 3-fold term here.

I just did as you suggested yestoday, adding a 2-fold generic term with
pk of zero. I attached the prmtop and frcmod files here. Nothing
surprising here. Everything is like what you said: the gaff 2-fold term
was zeroed and the 3-fold term was added.

What I can't explain is the 2-fold term in gaff seems to only add a
constant to the total energy, as you can see from tmp.jpg. The red line
is calculated with and the black one is calculated with


David A. Case wrote:
> On Wed, Jun 29, 2005, Guanglei Cui wrote:
>>The zeroed c3-os-p5-o term (see 
>> was introduced as a 3-fold term with zero pk in frcmod, and
>>it did replace the 2-fold generic term in gaff (see
> I'm still lost here.  Yesterday, you posted a prmtop file (called
> "") where there were clearly *both* 2-fold and 3-fold terms
> C1-O1-P1-O2.  Today, your "" has only three-fold terms.  But
> can't tell what you did differently between yesterday and today....
> ...dac

(image/jpeg attachment: tmp.jpg)

Received on Wed Apr 05 2006 - 23:49:55 PDT
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