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

From: FyD <>
Date: Wed, 07 Sep 2005 14:40:25 +0200

Quoting Cenk Andac <>:

> 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.

ups I forgot something here, sorry...
The default GAMESS algo. used in geom. opt. for metal complexes is not used when
executing R.E.D.-II/III. This is has been carried out to get indentical results
using either Gaussian or GAMESS.

For more information, please see R.E.D.-II manual page 16
and in R.E.D.-II line 510, you might prefer to use:
if ($TestL4a == 1){ print JOB1_FILE "COORD=UNIQUE \$END\n"; }
instead of
if ($TestL4a == 1){ print JOB1_FILE "ISPHER=1 COORD=UNIQUE \$END\n"; }

> The version of GAMESS I use is
> "GAMESS VERSION = 19 MAY 2004 (R4)".
> Therefore, I changed three lines in
> saying "all processes have ended gracefully" to
> "exited gracefully".
> Now, RED-II works just fine. Thanks for letting me
> know about

oh oh here I do not understand you "all processes have ended gracefully" is
This means you modified R.E.D.-I or I am lost ;-)

Finally using the message generated by ddikick might mot be a good idea or at
least not compatible with all the machines since I heared some machines do not
use ddikick; see R.E.D.-II manual page 8

regards, Francois

 • F.-Y. Dupradeau •
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
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Received on Wed Sep 07 2005 - 13:53:00 PDT
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