Re: Antechamber generating bad charges w/ gaussian 98.

From: James W. Caldwell <>
Date: Wed 23 Oct 2002 16:16:05 -0700 (PDT)

What do the intermediate files look like? Especially what are the
ESP charges from your gaussian run? They should be similar.


On Wed, 23 Oct 2002, Nicholson, James D Mr ARO wrote:

>I am trying to generate charges for a modified nucleic base using
>Antechamber and the RESP protocol. However, the charges are highly
>exagerated. In many cases the charges are have changed sign from what is
>found in the corresponding parm98 unit or in the mopac calculation for the
>same molecule.
>I'm getting methyl hydrogens having partial charges of -2.51!
>Here are the steps I used to create this mess:
>1) Created model in insight
>2) Minimized using mopac interface in insight environment
>3) "antechamber -i <input file> -fi mol2 -o <output> -fo gcrt"
>4) Edited the output of antechamber to only run optimization, since, I was
>having problems w/ Gaussian crashing. I basically ran the input through a
>Gaussian (g98) minimization by changing the first link to:
> UHF/6-31G* Test opt SCFCYC=256
>5) Took the optimized output and ran a single point resp calculation with
>first link being:
> UHF/6-31G* Test SCF=Tight Pop=MK iop(6/33=2) iop(6/42=6)
>which is basically the antechamber-generated file w/o the optimization.
>6) Calculated charge w/ the following command.
> antechamber -i <gaussian .out> -fi -gout -o <prep file> -fo -prepi
>-c resp
>7) Examined the prep file w/ xleap to discover the bad charges.
>The problems seem to be most pronounced along a stretch of extended alkyl
>chain. I remember in some of the papers that this can be a problem.
>However, there are problems all over.
>Could this be a units mismatch between Gaussian and amber? Gaussian is
>working in Hartree-Bohr-Radians. I doubt it, but, need to mention it as a

James W. Caldwell                         (voice) 415-476-8603
Department of Pharmaceutical Chemistry    (fax)   415-502-1411  
Mail Stop 0446                            (email)
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University of California                  
San Francisco, CA 94143-0446               
Received on Wed Oct 23 2002 - 16:16:05 PDT
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