RE: AMBER: Electrostatic Energy Components

From: Ross Walker <>
Date: Fri, 21 Nov 2008 16:20:56 -0800

> Thanks for your explanations, but I could not understand this paragraph
> of yours. Let's say we have created a nice QM profile of a particular
> torsion. To do the fitting, the MM energy without the dihedral energy of
> this particular torsion should be calculated (let's call it MM_1). This
> means that an frcmod file with zero torsional barrier of the particular
> torsion needs to be used. Then, QM-MM_1 is calculated, which is fitted to
> the desired cosine terms. If the fitting will include 2 cosine terms, for
> example, QM-MM_1 should be fitted to V_1 * (1+cos(n1*x)) + V_2 *
> (1+cos(n2*x)).
> In the whole above process, the 1-4EEL and VDW terms are not
> used/calculated explicitly. They are included in the MM_1
> energy implicitly. Did you mean that? Thanks.

Indeed... you are doing it the 'correct' way. What I was referring to was
that I have seen examples where people skip the MM with zero torsion step
and simply adjust their QM energy by an 'origin' of some description and
then fit the torsion profile to that - hence completely neglecting the 1-4
EEL and VDW terms.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | 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.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Fri Dec 05 2008 - 16:18:18 PST
Custom Search