AMBER Archive (2004)

Subject: AMBER: peoblemwith RED II

From: anshul_at_imtech.res.in
Date: Tue Aug 17 2004 - 14:15:30 CDT

Hi amber users,
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 forthe charge calculation. 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). 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 RED-vII.pl

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
RED-vII.pl 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?

Any suggestions are highly appreciated.

With regards,

Anshul Awasthi
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India.
Mobile +91-9872220352

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