AMBER Archive (2005)

Subject: Problem solved! Re: AMBER: How to get PDB structures optimized for RED-II

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Sat Oct 22 2005 - 12:38:58 CDT

Hi Francois,

I have installed the latest version of GAMESS (27 JUN
2005 (R2)) on my PC-LINUX computer. RED II has now no
problems with the new version of GAMESS.
I ran a GAMESS job for a copper.4H2O complex using
REDII's default optimization parameters. I has taken
about more than two days and finally I got my ESP
charges and a mol2 structure for the optimized complex
so this case is closed.
As a result, I have decided to upgrade my PIII-800 MHz
computer to a higher speed such as PIV-3.0 GHZ or
above.

I am now working on restraining ESP charges for the
copper complex.I plan on sending you another E-Mail
for that.

thanks,

Jenk.
           

--- FyD <fyd_at_u-picardie.fr> wrote:

> Quoting Cenk Andac <cenk_andac_at_yahoo.com>:
>
> > 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 RED-II.pl
> > saying "all processes have ended gracefully" to
> > "exited gracefully".
> > Now, RED-II works just fine. Thanks for letting me
> > know about
> >
> http://www.u-picardie.fr/labo/lbpd/RED/FAQ-II.htm#2.
>
> oh oh here I do not understand you "all processes
> have ended gracefully" is
> checked by R.E.D.-I and "EXECUTION OF GAMESS
> TERMINATED NORMALLY" by R.E.D.-II
> 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
> ••••
> http://www.u-picardie.fr/labo/lbpd/FyD.htm
>
-----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to
> majordomo_at_scripps.edu
>

Cenk Andac, M.S., Ph.D. Dissertator
at the University of Wisconsin-Madison
 
Currently a faculty candidate in Turkey
Address:
Guleryuz cad. 37/15, Ankara, Turkey
90-(312)-4281941
E-Mail:cenk_andac_at_yahoo.com

        
                
__________________________________
Yahoo! Mail - PC Magazine Editors' Choice 2005
http://mail.yahoo.com
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu