Dear Francois
>If I remember the SCRF'IEFPCM' solvation model in G03 is different to
>that in g09: I would use in your case, Gaussian 2003.
Now, I am using g03.
>Did you try to use both approaches? (I am sure we tested that,
>but I forgot...)
>Is there any difference?
I have tried the both approaches and found differences.
I used CH3SOCH3 as an example target molecule.
RESP charges of the resultant mol2 files are as follows:
epsilon=4.0 approach
1 C1x y z C1 1-0.1752 ****
2 H2x y z H2 10.1040 ****
3 H3x y z H3 10.1040 ****
4 H4x y z H4 10.1040 ****
5 S5x y z S5 10.2220 ****
6 O6x y z O6 1-0.4844 ****
7 C7x y z C7 1-0.2301 ****
8 H8x y z H8 10.1186 ****
9 H9x y z H9 10.1186 ****
10 H10x y z H 10 10.1186 ****
Solvent=Ether approach
1 C1x y z C1 1-0.1749 ****
2 H2x y z H2 10.1042 ****
3 H3x y z H3 10.1042 ****
4 H4x y z H4 10.1042 ****
5 S5x y z S5 10.2216 ****
6 O6x y z O6 1-0.4860 ****
7 C7x y z C7 1-0.2294 ****
8 H8x y z H8 10.1187 ****
9 H9x y z H9 10.1187 ****
10 H10x y z H 10 10.1187 ****
where, I omitted actual coordinates.
If a target molecule is charged, differences may be larger.
I have not calculated that kind of molecules, though.
Although I have no idea which way amber 03 was actually derived,
I have found a document where Yong Duan referred to the subject.
http://structbio.vanderbilt.edu/archives/amber-archive/2005/1290.php
It seems Solvent=Ether would be appropriate.
Thank you for your kind suggestion and responses!
best regards,
Shuntaro
(2011/05/18 20:17), FyD wrote:
> 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 Thu May 19 2011 - 01:30:03 PDT
