AMBER Archive (2005)

Subject: Re: AMBER: RED-II failure to recognize GAMESS output

From: Cenk Andac (cenk_andac_at_yahoo.com)
Date: Tue Sep 06 2005 - 03:30:19 CDT

Hi Francois,

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.

regards,

jenk

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

> Quoting Cenk Andac <cenk_andac_at_yahoo.com>:
>
> > I have been using Red-II to determine RESP charges
> > for the NMeacetamide (NMA) example in RED-II
> manual
> > (p26). I used GAMESS to optimize coordinates for
> NMA.
> > I also used the following set-up in RED-II for the
> > optimization process.
> >
> > $XRED = "Off";
> > $NP = "1";
> > $QMSOFT = "GAMESS";
> > $OPT_Calc = "On";
> > $MEPCHR_Calc = "On";
> > $CHR_TYP = "RESP";
> > $CHR_VAL = "0";
> > $MLT_VAL = "1";
> > $TITLE = "nacet";
> > $DIR = "~/dir";
> > $MOL_START = "~/dir/nacet.pdb";
> > $JOB_OPT = "~/dir/JOB1-gam1.log";
> >
> > In principal, GAMESS minimized NMA and printed
> > out JOB1-gam1.irc and JOB1-gam1.dat files in
> gamess'
> > src directory.
>
> For using GAMESS & R.E.D. please see the R.E.D.-II
> manual, pages 7-8.
> i. e. 'Remarks regarding the use of "GAMESS" with
> R.E.D.'
> Just in case ;-)
>
> > Here are some words in ~/dir/JOB1-gam1.log file:
> > JOB1-gam1.log:
> > ************************************
> > 1 ***** EQUILIBRIUM GEOMETRY LOCATED *****
> > COORDINATES OF ALL ATOMS ARE (ANGS)
> > ATOM CHARGE X Y Z
> >
> ----------------------------------------------------
> > C 6.0 2.0074569211 1.0062470751
> 0.0000000000
> > H 1.0 1.6249586848 -0.0033937275
> 0.0000000000
> > H 1.0 1.6413208735 1.5288656361
> 0.8781704037
> > H 1.0 1.6413208734 1.5288656362
> -0.8781704038
> > C 6.0 3.5222773671 0.9566272924
> 0.0000000000
> > O 8.0 4.1288339649 -0.0788038913
> 0.0000000000
> > N 7.0 4.1252034162 2.1701985420
> 0.0000000000
> > H 1.0 3.5523591717 2.9823246679
> 0.0000000000
> > C 6.0 5.5597011361 2.3455464160
> 0.0000000000
> > H 1.0 6.0184115984 1.3701706433
> 0.0000000000
> > H 1.0 5.8850779964 2.8876758549
> -0.8816339325
> > H 1.0 5.8850779964 2.8876758549
> 0.8816339325
> > [...]
> >
> > ----------------------------------------
> > CPU timing information for all processes
> > ========================================
> > 0: 454.256942 + 19.266071 = 473.523013
> > ----------------------------------------
> > ddikick.x: exited gracefully.
> > ----- accounting info -----
> > Fri Sep 2 20:23:49 PDT 2005
> > ...
> > ***************************************
> >
> > Although NMA was optimized by GAMESS,
> > RED-II gave me the following error message.
> >
> > * Software checking *
> > rungms [ OK ]
> > gamess.01.x [ OK ]
> > ddikick.x [ OK ]
> > resp [ OK ]
> > The structure/conformation(s) is/are being
> optimized
> > [ FAILED ]
> > See the file "JOB1-gam1.log"
> > Press Enter to exit
>
> I think the way you use R.E.D. is correct...
>
> There is a trick anyway somewhere, please see
> http://www.u-picardie.fr/labo/lbpd/RED/FAQ-II.htm#2
> to understand the GAMESS||Gaussian format recognized
> by R.E.D.
> - The author names are checked to differentiate
> GAMESS and Gaussian output
> (since, with R.E.D.-II, geom. opt. output from
> Gaussian can be used in MEP
> computation with GAMESS, and vis-versa)
> - EQUILIBRIUM GEOMETRY LOCATED is checked for
> GAMESS
> - EXECUTION OF GAMESS TERMINATED NORMALLY is also
> checked for GAMESS...
>
> I just did a test with MeOH and it worked fine. What
> is the GAMESS version you
> use ? The version I used is "GAMESS VERSION = 22 NOV
> 2004 (R1)"
>
> > I then re-ran RED-II this time by turning off
> > "OPT_calc" option and using JOB1-gam1.log as input
> >
> > $XRED = "Off";
> > $NP = "1";
> > $QMSOFT = "GAMESS";
> > $OPT_Calc = "Off";
> > $MEPCHR_Calc = "On";
> > $CHR_TYP = "RESP";
> > $CHR_VAL = "0";
> > $MLT_VAL = "1";
> > $TITLE = "nacet";
> > $DIR = "~/dir";
> > $MOL_START = "~/dir/nacet.pdb";
> > $JOB_OPT = "~/dir/JOB1-gam1.log";
> >
> > This time, RED-II gave the following error
> > message :
> >
> > * Selected QM Software *
> > GAMESS
> > * Selected optimization output *
> > GAMESS
> > Invalid optimization OUTPUT !
> > Press Enter to exit.
> >
> > Could anyone of you please let me know why
> > RED-II does not recognize the GAMESS output
> > (JOB1-gam1.log)?
>
> Same rules (as above) are applied here with this new
> one:
> - The atom order (& _chemical elements_) in the
> initial PDB file & in the QM
> output must be the same.
>
> Finally, you could try the following variables:
> $OPT_Calc = "Off";
> $MEPCHR_Calc = "On";
> $DIR = "~/dir";
> $MOL_START = "./nacet.pdb";
> $JOB_OPT = "./JOB1-gam1.log";
>
> Indeed, at the end of the R.E.D. job "dir" is
> renamed into "dir-1", and your new
> directory which contains your charges is "dir" (see
> the 'Remark' in the
> R.E.D.-II manual page 27).
>
> Tell me if it works now, 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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