Re: AMBER: peoblemwith RED II

From: FyD <>
Date: Thu, 26 Aug 2004 17:44:16 +0200

Dear Anshul,

> I am using RED II for the multiorientation multiconformation RESP charge
> calculation. I used 2 conformations and 5 orientations for this purpose.
> After the minimization of 2 conformations, I concatenated the 2 .log files
> in single file.


> Then I ran the RED for the charge calculation.

This means you used:
$OPT_Calc = "Off";
$MEPCHR_Calc = "On";
$JOB_OPT = "your_path/your_concatenated_file.log";

> the problem
> I faced was that after the calculations for the first molecule the process
> stopped as the scratch directory of GAMESS was not empty (contained .dat
> file).

This means a former GAMESS job was killed by someone and some temporary files
remained in this scratch directory...

I created the following variable in my ".cshrc" file:
setenv SCR /disk2/QM_SCR

Then, each time I get such ERROR message from R.E.D.
"ERROR: Scratch directory is NOT empty"

I execute "rm $SCR" and then I re-run R.E.D.

> to rectify this problem I renamed the *.dat file in the scratch
> directory to *.pun; after the gamess.00.x execution is over.
> mv /usr/people/anshul/misc/GAMESS/gamess/temp/JOB2-gam1.dat
> /usr/people/anshul/misc/GAMESS/gamess/temp/JOB2-gam1.pun
> and also made changes in the

ouf... you should NOT modify the R.E.D.-II source code for this
but simply read the FAQ-39.

> After this the RED process was running nicely and completed the MEP
> calculations.
> ------------------------------------------------------------------------
> The MEP is/are being computed ...
> Conformation 1 ... [ OK ]
> See the file(s) "JOB2-gam1-(X).pun"
> Conformation 2 ... [ OK ]
> See the file(s) "JOB2-gam2-(X).pun"
> ------------------------------------------------------------------------
> but after this when the programme tried to derive the RESP charges, it
> failed:
> ---------------------------------------------------------------------
> The RESP charges are being derived ... [ FAILED
> See the "punch2" and "output(1|2)" files
> ---------------------------------------------------------------------
> The output and punch files showed the following error:
> ---------------------------------------------------------------------
> 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
> ----------------------------------------------------------------------
> I red in the FAQ of RED that this error is because RED did not find .dat
> files in the scratch directory of GAMESS. I changes the .dat files in teh
> file to .pun but still it ended with the same error.
> Can anyone tell me how to deal with this. if i keep te .dat files then it
> does not run and if i rename it, it still does not run to completion. Is
> there anyother way by which we can handel these problems?

Then if you still have this problem look at the end of the RESP ouputs
(i.e. "output1" and/or "output2" files) you might find an error message coming
from the RESP program itself.

With R.E.D.-II, multi-orientation and multi-conformation can be performed in
same time this means that the number of center increase a lot.
And from what we checked there is a limitation in RESP to 500 centers...
Read the bug-5 for a discussion about this problem

Check the number of centers you have i.e
$atoms * $i conformations * $j orientations
If you are above 500, look at the RESP source code and try to increase this
number or
simply use 2 conformations and only 4, 3 or 2 orientations...

Regards, Francois

F.-Y. Dupradeau
Faculte de Pharmacie, UPJV, Amiens, France
The Scripps Research Institute, San Diego, USA
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Received on Thu Sep 02 2004 - 01:15:11 PDT
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