AMBER Archive (2005)

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

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Fri Oct 14 2005 - 12:14:02 CDT

 Dear amber members,
 
I set OPTTOL=1.0E-05 and removed ISPEHRE=1 in
lines 510 and 916 in REDII (beta version) and ran a
redii and GAMESS job for a Cu+ complex coodinated
to 4 TIP3 water molecules. I set multiplicity for the
complex to 1 in redii.
  
 Unfortunately, the red-ii job (with suggested
 parameters attached in an E-mail response below) did
not geometry
 optimize the copper complex.I had to kill the redii
job after it ran for about one day.
 Would anyone have any idea as to what might be wrong
with the redii setup?
 
 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
> >
>

        
                
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