AMBER: How to get PDB structures optimized for RED-II

From: Cenk Andac <>
Date: Tue, 6 Sep 2005 01:49:13 -0700 (PDT)

Dear amber members,

I have been working on computing RESP charges for an
aminoacid-copper complex using redII and GAMESS.
I prepared a PDB file for the complex in LEAP and
relaxed it using LEAP's relax option.
However, GAMESS has failed optimizing the complex
strucuture for more than 2 days. Obvioulsly the
structure does not converge to 1.E-8.
I know that RED-II and GAMESS have passed a test run
with NMethylacetamide provided in RED-II manual. I
have also triple checked connectivity and ATOM
information in the PDB file for the complex. There is
no problem with that either.
The problem is I think with atomic coordinates. I
guess I need to start out with a converged structure
(~1.E-8) of the complex.

Currently, I do not have such a commercially available
expensive facility to do that. I was wondering if
anyone of you can suggest me a free version of an MD
software to prepare converged structures that would
work with RED-II and GAMESS.

best regards,


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Received on Tue Sep 06 2005 - 09:53:01 PDT
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