Shuntaro,
>> 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 .
http://q4md-forcefieldtools.org/REDS/ is limited to
150 atoms
- R.E.D. Server Development .
http://q4md-forcefieldtools.org/REDS-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 RED-vIII.4.pl (to which Corn2Duan.csh have been already applied)
> generates.
ok
> ‘#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...
.
http://www.gaussian.com/g_tech/g_ur/k_scrf.htm
DiethylEther: ε=4.2400
.
http://en.wikipedia.org/wiki/Diethyl_ether_(data_page)
DiethylEther: ε0 = 4.34 at 20 °C
Did you try to use both approaches? (I am sure we tested that, but I
forgot...)
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
>>> ‘http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php’.
>>> However, I bumped into a problem in the stage of Gaussian jobs of
>>> ‘perl RED-vIII.4.pl’. 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 RED-vII.4.pl will make,
>>> then execute RED-vIII.4.pl with commenting out
>>> “system("$gauss JOB1-gau_m$NM-$NC.com");” in RED-vIII.4.pl.
>>> 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 (http://ambermd.org/bugfixesat.html)
>>>>> <http://ambermd.org/bugfixesat.html%29>‘,
>>>>> “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 http://q4md-forcefieldtools.org/
>>>>
>>>> regards, Francois
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Received on Wed May 18 2011 - 04:30:02 PDT
