Re: [AMBER] Using Gaussian 09 (g09), how can I obtain RESP charges of a new residue?

From: FyD <>
Date: Wed, 18 May 2011 13:17:02 +0200


>> Why not using R.E.D. Server? any researcher can use 8 cpu cores...
> Thank you for your offer.
> However my target molecule consists of over 100 atoms
> and number of initial structures will be no less than 10.

- R.E.D. Server . is limited to
150 atoms
- R.E.D. Server Development . is limited to 350
atoms; but... You should consider spilling your big molecule into more
elementary(smaller) building blocks.

> By the way, the following lines are quoted from the Gaussian input
> that (to which Corn2Duan.csh have been already applied)
> generates.


> ‘#P b3lyp/cc-pVTZ SCRF(IEFPCM,Solvent=Ether) SCF(Conver=6) NoSymm Test
> Pop=mk IOp(6/33=2) GFInput GFPrint’

If I remember the SCRF'IEFPCM' solvation model in G03 is different to
that in g09: I would use in your case, Gaussian 2003.

> Why do they use Solvent=Ether,
> not SCRF(IEFPCM, Read) with input section for PCM keywords (eps=4.0)?
> In deriving RESP charges compatible with Amber 03 force field,
> we should use B3LYP/cc-pVTZ method with IEFPCM (epsilon=4.0).
> (Duan et al. Vol. 24, No. 16. Journal of Computational Chemistry)

I see what you mean...

DiethylEther: ε=4.2400
DiethylEther: ε0 = 4.34 at 20 °C

Did you try to use both approaches? (I am sure we tested that, but I
Is there any difference?

regards, Francois

> (2011/05/18 18:03), FyD wrote:
>> Dear Suntaro,
>>> Thank you for your reply.
>>> I have introduced R.E.D. III.4 tools with g03 rev E.1.
>>> I want to derive RESP charges of a new residue which are compatible with
>>> Amber 03 force field using many initial conformations.
>>> So I am conducting the series of commands described in
>>> ‘’.
>>> However, I bumped into a problem in the stage of Gaussian jobs of
>>> ‘perl’. The problem is that it takes too much time.
>> Why not using R.E.D. Server? any researcher can use 8 cpu cores...
>>> So I am going to execute the Gaussian jobs in advance
>>> where the log files are named after those will make,
>>> then execute with commenting out
>>> “system("$gauss JOB1-gau_m$NM-$");” in
>>> Can this have a bad effect on the procedure for making RESP charges?
>> Yes, you can do that (however, provide the correct file name_s_ IN
>> AGREEMENT WITH THE P2N FILE)- we did exactly that for a user ;-)
>> This corresponds to a pseudo "Re-fit" mode...
>> regards, Francois
>>> (2011/05/16 15:07), FyD wrote:
>>>> Dear Chiba Suntaro,
>>>>> I am deriving RESP charges of a new residue using Gaussian 09 rev B.01
>>>>> (g09).
>>>>> According to ‘AmberTools Bug Fixes (
>>>>> <>‘,
>>>>> “In Gaussian09 rev B.01, the facility to write out the electrostatic
>>>>> potential
>>>>> on a grid of points was inadvertently deleted.”
>>>> - You could use the R.E.D. III.4 tools with GAMESS or Firefly, or
>>>> - You could also use R.E.D. Server 2.0, which interfaces GAMESS,
>>>> Firefly or Gaussian 09 version A2 (or Gaussian 3003 version E.01).
>>>> See
>>>> regards, Francois

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Received on Wed May 18 2011 - 04:30:02 PDT
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