AMBER Archive (2008)

Subject: Re: AMBER: Need help... High energies for complex...

From: Carlos Simmerling (
Date: Wed Sep 03 2008 - 06:27:06 CDT

did you use the same minimization procedure on the complex?

On Wed, Sep 3, 2008 at 7:20 AM, Waqas Nasir <> wrote:
> Hi,
> Hope every one is doing fine.
> Well, I have done some manual single point energy calculations on my protein
> carbohydrate complex using amber version 8. The protein is a dimmer and the
> sugar is a tetra-saccharide. The values for the binding energy that I am
> getting are quite high and are in the order of negative 3500-4500 kcal.
> The script that I have used breaks each of 250 frames in my md run into
> separate protein and sugar subunits. Minimization of about 500 steps is then
> performed on each subunit followed by single point md (one with 0 time
> steps). The energies from sugar and protein md runs for a single frame are
> added up. The difference of this value is then taken with the actual energy
> of the complex, that results is ridiculously high values.
> Just wanted to have some thoughts on what might have gone wrong in these
> calculations. Or, what steps one might take to improve the results in
> general.
> Any sort of check list is highly appreciated.
> Thanks a lot for reading...
> Stay blessed!
> Regards,
> Waqas.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
CMM Bldg, Room G80
Stony Brook University E-mail:
Stony Brook, NY 11794-5115 Web:
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