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

From: David A. Case <>
Date: Wed, 29 Jun 2005 11:12:25 -0700

On Wed, Jun 29, 2005, Guanglei Cui wrote:

> 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 guess I am trying to find out *exactly* what you did: the exact leap
commands, the exact frcmod files, etc.

I don't care anything about the particular problem, or about whether terms
zero or not. The confusing thing is that you have posted three topology
in the past two days. Two of those have *both* two-fold and three-fold
torsions for the C-O-P-O angles. One of the them had *only* the
torsion. I'm trying to figure out what is happening.

I think we are thinking about different things. Above you say "the
2-fold term was replaced by this specific three-fold term", but that does
*not* seem to be the case: in "" file indicates that the original
2-fold term was replaced by a new *2-fold* term (not by a three-fold
and then the new 3-fold term was added (so that you get both).

I still suspect that when you created the prmtop file with no 2-fold term
all, that you actually did something different than what you are
But I'd like to be sure.

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