AMBER Archive (2009)

Subject: [AMBER] Compatibility of ONIOM and Amber

From: vaibhav dixit (vaibhavadixit_at_gmail.com)
Date: Fri Dec 18 2009 - 00:30:32 CST

Dear Friends,
Recently we wanted to compute the binding energies of a few ligands for
their proteins and try to correlate with biological activity.

For this we decided to combine Docking and ONIOM (Gaussian03) results.
(based on J. Chem. Inf. Model. 2009, 49, 886-899)

In the ONIOM jobs the single point (HF/6-31+G(d):UFF=QEQ) calculations are
working properly.

But when we tried to use the Amber force field, Gaussian03 in not able to
set parameters by itself even for the only protein files (where ligand has
been removed manually and there are only protein atom present with no water
or hereto atom present). How to fix this?

Also we came across some report within amber community that use of Amber
force fields within Gaussian is not such a good idea. Why this is so? and
what are the options for combing Amber and ONIOM? please suggest !!!

 http://archive.ambermd.org/200908/0170.html

--------------------------------------
>4) Gaussian Oniom method = a way of doing optimizations with different
>levels of theory. Be aware DO NOT use the AMBER force field in Gaussian!!!
>It is crazy old and very broken!
------------------------------------ 

-- 
With regards

Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
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