Dear Francois,
>- The two methyl groups do not bear the same charge values. I guess
>you used Ante_R.E.D. 1.4, which does know how to deal with chemical
>equivalencing between different chemical groups. Use R.E.D.
>Server/Ante_R.E.D. 2.0 to solve this problem.
Yes. I used Ante_R.E.D. 1.4.
I did not notice that point (chemical equivalency).
I have registered in R.E.D. Server. I am going to try it.
I really appreciate your remarks.
best regards, Shuntaro
(2011/05/20 16:43), FyD wrote:
> Dear Shuntaro,
>
>> 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 > Solvent=Ether approach
>> 1 C1x y z C1 -0.1752 **** versus > 1 C1x y z C1 -0.1749 ****
>> 2 H2x y z H2 0.1040 **** versus > 2 H2x y z H2 0.1042 ****
>> 3 H3x y z H3 0.1040 **** versus > 3 H3x y z H3 0.1042 ****
>> 4 H4x y z H4 0.1040 **** versus > 4 H4x y z H4 0.1042 ****
>> 5 S5x y z S5 0.2220 **** versus > 5 S5x y z S5 0.2216 ****
>> 6 O6x y z O6 -0.4844 **** versus > 6 O6x y z O6 -0.4860 ****
>> 7 C7x y z C7 -0.2301 **** versus > 7 C7x y z C7 -0.2294 ****
>> 8 H8x y z H8 0.1186 **** versus > 8 H8x y z H8 0.1187 ****
>> 9 H9x y z H9 0.1186 **** versus > 9 H9x y z H9 0.1187 ****
>> 10 H10x y z H10 0.1186 **** versus > 10 H10x y z H10 0.1187 ****
>>
>> where, I omitted actual coordinates.
>> If a target molecule is charged, differences may be larger.
>> I have not calculated that kind of molecules, though.
>
> Two remarks:
>
> - The two methyl groups do not bear the same charge values. I guess
> you used Ante_R.E.D. 1.4, which does know how to deal with chemical
> equivalencing between different chemical groups. Use R.E.D.
> Server/Ante_R.E.D. 2.0 to solve this problem. Please, read:
> http://q4md-forcefieldtools.org/REDS/popup/popanteredtopequiv.php
>
> - The differences you report seems quite small...
>
>> 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.
>
> 'appropriate'...: at least, it seems this is the g03 keyword that was
> used ;-)
>
> If you continue to read this '1290.php' email, you can see that ff03
> charge values can not be reproduced. This point has been discussed
> many times in the Amber mailing list, and this is the main reason why
> R.E.D. (and then R.E.DD.B. & R.E.D. Server) was develop: to derive
> reproducible charges; your charge values will be reproducible by other
> researchers only if you use R.E.D.
>
> regards, Francois
>
>
>
>
>> (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 Fri May 20 2011 - 02:30:03 PDT
