AMBER Archive (2007)

Subject: AMBER: gaussian output to prepin problem

From: Rima Chaudhuri (rima.chaudhuri_at_gmail.com)
Date: Mon Jan 29 2007 - 11:14:31 CST

Hello!

I am trying to generate topology files for a ligand. I ran gaussian and
tried to generate the prepin file from the .gout (gaussian output), on
checking the output i.e. the .prepin file, it seems that the charges are not
being read and the last column remains to be 0.000.

Hence, I tried to use the following command (step by step approach)

antechamber -fi gout -fo ac -i resp631_GSJ.out -o respgen_GSJ_input.ac -c
resp

 Amber8 Module: resp

forrtl: severe (24): end-of-file during read, unit 5, file
/home/rchaud/gaussian/ANTECHAMBER_RESP1.IN
Image PC Routine Line
Source
resp 080A90B4 Unknown Unknown Unknown
resp 080A7C8C Unknown Unknown Unknown
resp 0808705D Unknown Unknown Unknown
resp 0805CB50 Unknown Unknown Unknown
resp 0805D027 Unknown Unknown Unknown
resp 0806B0BA Unknown Unknown Unknown
resp 0804A69B Unknown Unknown Unknown
resp 0804A4BA Unknown Unknown Unknown
resp 0804A341 Unknown Unknown Unknown
Unknown 00134E33 Unknown Unknown Unknown
resp 0804A271 Unknown Unknown Unknown

 Amber8 Module: resp

forrtl: severe (24): end-of-file during read, unit 5, file
/home/rchaud/gaussian/ANTECHAMBER_RESP2.IN
Image PC Routine Line
Source
resp 080A90B4 Unknown Unknown Unknown
resp 080A7C8C Unknown Unknown Unknown
resp 0808705D Unknown Unknown Unknown
resp 0805CB50 Unknown Unknown Unknown
resp 0805D027 Unknown Unknown Unknown
resp 0806B0BA Unknown Unknown Unknown
resp 0804A69B Unknown Unknown Unknown
resp 0804A4BA Unknown Unknown Unknown
resp 0804A341 Unknown Unknown Unknown
Unknown 00134E33 Unknown Unknown Unknown
resp 0804A271 Unknown Unknown Unknown
Cannot open charge file QOUT , exit

Both the resp1 and resp2.in files are empty.
Our guess is that the gout(gaussian output file) has something erroneous, on
checking we found that the ESP fit runs past 9999 and this might generate
trouble!?
      ESP Fit Center 9999 is at -3.121005 2.016179 -4.380049
      ESP Fit Center **** is at -3.482138 2.224679 -4.380049
      ESP Fit Center **** is at -3.881619 2.344276 -4.380049
      ESP Fit Center **** is at -4.297913 2.368523 -4.380049
      ESP Fit Center **** is at -5.881150 1.189846
-4.380049...................
      .........................

We are trying to use the step by step appraoch from start instead of using
antechamber to generate the prepin from the gout, but is there any other way
we can modfiy any input command such that the the ESP fit runs more than the
default 9999 cycles ??
Any suggestions will be much appreciated.

Thanks

-Rima Chaudhuri
Dept. of Bio. Engg.
Bioinformatics Program - PhD candidate
University of Illinois at Chicago

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