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

From: Guanglei Cui <cuigl.csb.sunysb.edu>
Date: Wed, 29 Jun 2005 11:47:39 -0700

OK. :)
Here is exactly how I created the prmtops.

source leaprc.gaff
loadamberparams frcmod
a = loadmol2 mmp.mol2
saveamberparm a prmtop inpcrd

mmp.gaff.top was created with no frcmod file;
mmp.new.top was created with frcmod.new;
mmp.nox.top was created with frcmod.nox;
b.top was created with frcmod2;

It seems to me a specific term will replace the general term (see
mmp.nox.top and mmp.gaff.top).

Guanglei

David A. Case wrote:
> 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 are
> zero or not. The confusing thing is that you have posted three topology
files
> 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
three-fold
> torsion. I'm trying to figure out what is happening.
>
> I think we are thinking about different things. Above you say "the
original
> 2-fold term was replaced by this specific three-fold term", but that
does
> *not* seem to be the case: in "b.top" file indicates that the original
> 2-fold term was replaced by a new *2-fold* term (not by a three-fold
term),
> 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 at
> all, that you actually did something different than what you are
reporting.
> But I'd like to be sure.
>
> ...thanks...dac
>




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