AMBER Archive (2007)

Subject: RE: AMBER: gaussian output to prepin problem

From: Junmei Wang (jwang_at_encysive.com)
Date: Mon Jan 29 2007 - 20:43:56 CST

Hi Rima,
Lines like "ESP Fit Center **** is at -5.881150 1.189846 -4.380049" in
gout should not produce an error. I would like to figure out what
happened if you send me your gout file.
 
Best
 
Junmei
 

        Subject: AMBER: gaussian output to prepin problem
        
        
        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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