Dear Francois,
>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.
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.
‘#P b3lyp/cc-pVTZ SCRF(IEFPCM,Solvent=Ether) SCF(Conver=6) NoSymm Test
Pop=mk IOp(6/33=2) GFInput GFPrint’
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)
Best regards, Shuntaro
(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 - 03:30:02 PDT
