Re: AMBER: frcmod

From: David A. Case <>
Date: Tue, 12 Jun 2007 14:34:35 -0700

On Tue, Jun 12, 2007, Brooke Elizabeth Adams wrote:

> In Amber 8, I am working with the molecule Phosphoramidocyanidic acid,
> dimethyl-,ethyl ester. The parm file, frcmod, does not have force field
> values for some bonds.

We need more information about what you really mean when you say "I am
working" with a certain molecule. Did you use antechamber? Or get the frcmod
file by some other method? If you used antechamber, please post the exact
command line you used, plus the input pdb file (or whatever was used.)
If you used some other method, you need to say what that was (and why you
didn't use antechamber.)

> CY - P5- NT
> nitrile C, P with four bonded atoms, n3
> and
> CY -P5 -os
> nitrile C, P with four bonded atoms, Os

You seem to have a strange mixture of upper-case and lower-case atom types,
and I can't tell how that came about. GAFF would always have all lower-case
atom types.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jun 13 2007 - 06:07:36 PDT
Custom Search