RE: amber-developers: Junmei weighs in on torsions

From: Ross Walker <>
Date: Thu, 30 Jun 2005 09:47:23 -0700

> So, my understanding was wrong, (although I still sort of
> agree with Tom's
> comments on halogens.) This means that the "rule" is that a
> specific one-fold
> term will replace a wild-card three-fold term. This is
> "good" in the sense
> that it is what LEaP does under most circumstances, so we do
> not need to think
> about undo-ing (or redo-ing) a big body of work.

But this seems to be the opposite to how Leap deals with frcmod files.
in parm99.dat there is:

X-C -CT-X 6 0.00 0.0 2.

Which for NMA should appear 6 times for 3 x HC-CT-C-O and 3 x HC-CT-C-N
although leap only actually writes 5 of these to the prmtop file 2 x
HC-CT-C-O and 3 x HC-CT-C-N. This is worrying as I doubt it is restricted
just something simple like NMA. It doesn't matter here as the value is
but even so, something is wrong.

Now, if I create an frcmod file with

HC-CT-C-O 1 2.5 180.0 3.

If my understanding is correct the 2 fold wild card term above should be
discarded for the 3 x HC-CT-C-O dihedrals but kept for the HC-CT-C-N term.
However, Leap still writes all 5 (should be 6) terms to the prmtop file as
well as writing my explicit term. So, is this not backwards to how it
with the actual parmxx.dat files???

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
Received on Wed Apr 05 2006 - 23:49:55 PDT
Custom Search