AMBER Archive (2008)

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

From: Waqas Nasir (nasirwaqas1983_at_yahoo.com)
Date: Wed Sep 03 2008 - 06:20:01 CDT

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.

      
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