Hi Francois,
I have 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 Cu+ coodinated to 4 TIP3
water molecules. A pdb file for the complex is given
below. Multiplicity for the complex is 1.
REMARK REORIENT 2 13 5 | 5 13 2 | 2 13 8 | 8 13 2 |
REMARK REORIENT 2 13 11 | 11 13 2 |
REMARK REORIENT 8 13 11 | 11 13 8 | 8 13 5 | 5 13 8 |
REMARK REORIENT 5 13 11 | 11 13 5 |
ATOM 1 O1 C4W 1 0.266 0.664 0.389 1.00 0.00
ATOM 2 H1 C4W 1 1.162 0.487 0.107 1.00 0.00
ATOM 3 H1 C4W 1 -0.002 1.429 -0.118 1.00 0.00
ATOM 4 O2 C4W 1 -0.534 -0.758 -1.438 1.00 0.00
ATOM 5 H2 C4W 1 -1.127 -1.471 -1.669 1.00 0.00
ATOM 6 H2 C4W 1 -0.871 0.002 -1.912 1.00 0.00
ATOM 7 O3 C4W 1 -0.143 -1.718 0.781 1.00 0.00
ATOM 8 H3 C4W 1 -0.726 -2.452 0.592 1.00 0.00
ATOM 9 H3 C4W 1 -0.234 -1.572 1.722 1.00 0.00
ATOM 10 O4 C4W 1 -2.028 -0.193 0.418 1.00 0.00
ATOM 11 H4 C4W 1 -2.310 0.608 -0.022 1.00 0.00
ATOM 12 H4 C4W 1 -2.072 0.015 1.351 1.00 0.00
ATOM 13 CU5 C4W 1 -0.610 -0.501 0.038 1.00 0.00
CONECT 13 1 4 7 10
CONECT 1 13 2 3
CONECT 2 1
CONECT 3 1
CONECT 4 13 5 6
CONECT 5 4
CONECT 6 4
CONECT 7 13 8 9
CONECT 8 7
CONECT 9 7
CONECT 10 13 11 12
CONECT 11 10
CONECT 12 10
END
Unfortunately, the redii job (with suggested
parameters for metal complexes) did not geometry
optimize my copper complex for more than 12 hours
(NSERCH=~90 in gam-JOB1.log). Would you have any idea
about what might be wrong with the redii setup?
thanks,
jenk.
--- FyD <fyd.u-picardie.fr> wrote:
> Quoting Cenk Andac <cenk_andac.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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Received on Sat Oct 08 2005 - 14:53:00 PDT
