AMBER Archive (2004)

Subject: AMBER: Re: Results from RED-II beta

From: FyD (fyd_at_u-picardie.fr)
Date: Sun Jul 18 2004 - 11:11:41 CDT

Dear Scott,

I forward you an email about how to use R.E.D. (and R.E.D. version II beta) with
GAMESS I sent in the GAMESS mailing list. In particular, you have to modify
"rungms" to put the "job2-gamX.dat" file (punch file) generated by GAMESS (i.e.
where is the MEP) in the scratch directory and not in the working directory...

Regards, Francois

PS
Please send such questions in the AMBER mailing list.

----- Forwarded message from FyD <fyd_at_u-picardie.fr> -----
    Date: Mon, 12 Jul 2004 19:20:45 +0200
    From: FyD <fyd_at_u-picardie.fr>
Reply-To: GAMESS <gamess_at_lists.ciw.edu>
 Subject: Re: [Gamess] failure to generate RESP charges
      To: fyd_at_u-picardie.fr

Hi,

> Meanwhile I tried to run RED with semiimperical basis set in GAMESS.

My personal opinion is that it is a bad idea...

> It
> worked out preaty fast but it took 725 steps to converge.

It means your starting structure was bad. It might be the reason why your
6-31G* optimization takes so much time...

> I would like to
> know if such a large calculation is normal or is there something wrong
> with my system and how can I check it. Next MEP was calculated
> successfully but it failed to calculate the final RESP charges. the puch
> file which was generated is as follows: Statistics of the fitting:
> The initial sum of squares (ssvpot) 0.000
> The residual sum of squares (chipot) 0.000
> The std err of estimate (sqrt(chipot/N)) NaN
> ESP relative RMS (SQRT(chipot/ssvpot)) NaN
> Dipole Moment (Debye)= 0.00000

"NaN" means not a number. Something did not work...

R.E.D. needs the GAMESS '.dat' file to transform the GAMESS MEP ouput format
into RESP format (if you did not modify the R.E.D. code). R.E.D. get this MEP
.dat from the GAMESS scratch directory.

See 'rungms':
set SCR=/disk2/QM_SCR # ~ line 33 of GAMESS rungms
# /disk2/QM_SCR is my scratch directory

We modified 'rungms' in a way that GAMESS save its MEP .dat file in this
scratch
($SCR) directory. Thus, R.E.D. find it easily and move it in the directory
where
you decide to save your charge data. See rungms ~ line 73-80

# file assignments.
# all binary files should be put on a node's local disk ($SCR directory),
# both ASCII punch files might be written by NFS to user's permanent disk
set echo
setenv EXTBAS /dev/null
setenv IRCDATA $SCR/$JOB.irc
setenv INPUT $SCR/$JOB.F05
setenv PUNCH $SCR/$JOB.dat
setenv AOINTS $SCR/$JOB.F08
setenv MOINTS $SCR/$JOB.F09
setenv DICTNRY $SCR/$JOB.F10
setenv DRTFILE $SCR/$JOB.F11

_______________________________________________
Gamess mailing list
Gamess_at_lists.ciw.edu
http://lists.ciw.edu/mailman/listinfo/gamess
http://www.msg.ameslab.gov/GAMESS/

----- End forwarded message -----

> Francois,
>
> Thank you for the program. Since I have tried it out twice and it
> seems to handle my mixed QM packages/files well. Thank you for the
> great work you do on it and for getting it to me to try out.
>
> In trying out the program, I did run into a problem that I am not
> sure if you can help or not. As the program ran the resp module it
> returning charges of 0.0000 for all the atoms and terminated
> abnormally. I looked at the originally gamess log file and the Mulliken
> charges seemed alright.
>
> Mulliken atomic charges:
> 1
> 1 H 0.206877
> 2 C -0.574959
> 3 H 0.171673
> 4 H 0.202505
> 5 C 0.756762
> 6 O -0.622391
> 7 N -0.825399
> 8 H 0.418021
> 9 C -0.027954
> 10 H 0.219726
> 11 C -0.488208
> 12 H 0.173068
> 13 H 0.166149
> 14 H 0.212026
> 15 C 0.793295
> 16 O -0.647848
> 17 N -0.837101
> 18 H 0.419061
> 19 C -0.037069
> 20 H 0.220139
> 21 C -0.310789
> 22 H 0.190956
> 23 H 0.184193
> 24 C -0.177690
> 25 H 0.167801
> 26 C -0.475429
> 27 H 0.171443
> 28 H 0.165980
> 29 H 0.140578
> 30 C -0.476890
> 31 H 0.167445
> 32 H 0.163568
> 33 H 0.159985
> 34 C 0.781181
> 35 O -0.634242
> 36 N -0.798407
> 37 H 0.394402
> 38 C -0.275261
> 39 H 0.186402
> 40 H 0.172825
> 41 H 0.203578
> Sum of Mulliken charges= 0.00000
> Atomic charges with hydrogens summed into heavy atoms:
> 1
> 1 H 0.000000
> 2 C 0.006096
> 3 H 0.000000
> 4 H 0.000000
> 5 C 0.756762
> 6 O -0.622391
> 7 N -0.407378
> 8 H 0.000000
> 9 C 0.191772
> 10 H 0.000000
> 11 C 0.063035
> 12 H 0.000000
> 13 H 0.000000
> 14 H 0.000000
> 15 C 0.793295
> 16 O -0.647848
> 17 N -0.418039
> 18 H 0.000000
> 19 C 0.183070
> 20 H 0.000000
> 21 C 0.064359
> 22 H 0.000000
> 23 H 0.000000
> 24 C -0.009888
> 25 H 0.000000
> 26 C 0.002572
> 27 H 0.000000
> 28 H 0.000000
> 29 H 0.000000
> 30 C 0.014107
> 31 H 0.000000
> 32 H 0.000000
> 33 H 0.000000
> 34 C 0.781181
> 35 O -0.634242
> 36 N -0.404005
> 37 H 0.000000
> 38 C 0.287543
> 39 H 0.000000
> 40 H 0.000000
> 41 H 0.000000
> Sum of Mulliken charges= 0.00000
>
> Could you help me see where I could adjust my files or look at the
> program to get result at the end? I have attached some of the files in
> case they may be of help in debugging this.
>
> Scott
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