Re: [AMBER] benzene-sulfonate (atom type for Sulfur)

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sat, 14 Jul 2012 12:11:33 +0200

Jio,

> Thanks, but sorry I am not still able to converge to the solution. I
> wish to use GAFF params but just not able to decide about atom type
> of S (s6 or sy).

~260 or ~250? & what about 255? ;-)
  & what about the SX atom type in capital letters in agreement with
parm99.dat?

to use gaff, I think it does not matter; try one and see how you can
reproduce experimental data with that...

regards, Francois


> Dear Jio,
>
>>> the key point here is the vdW parameters for the sulfur atoms; but 
>>> they are all the same ;-)
>>
>> Yes I agree, but e.g. what about other params, say the lengths. I 
>> think ca-sy < ca-s6 because of the partial double bond character 
>> induced (please correct me if wrong). So still I am confused which 
>> one is correct to use.
>>
>> ca-s6  263.9    1.759        SOURCE1   229    0.0030    0.0036
>> ca-sy  247.7    1.784        SOURCE3    13    0.0068    0.0094
>
> I would develop a new frcmod file adapted to the RSO3(-) molecule...
>
> 1) geometry optimization by QM using a large basis set/theory level 
> for equilibrium values (or from X-ray structures)
>
> 2) develop new FF constants or adapt existing ones; my feeling is that 
> the accuracy of 263.9 or 247.7 is meaningless: It should be ~260 or 
> ~250 after a fit making the value general (see values in parm99.dat)...
>
> regards, Francois
>
>
>> Dear Jiom,
>>
>>> I have some query regarding atom type for Sulfur in case of Benzene 
>>> sulfonate (PhSO3- Na+). In gaff s6 (S with four connected atoms) and 
>>>   sy (Special s6 in conjugated systems) are there.
>>
>> the key point here is the vdW parameters for the sulfur atoms; but 
>> they are all the same ;-)
>>
>> parm99
>>    S           2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>    SH          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>
>> gaff:
>>    s           2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>    s2          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>    s4          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>    s6          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>    sx          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>    sy          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>    sh          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>    ss          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>
>> regards, Francois



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Received on Sat Jul 14 2012 - 03:30:02 PDT
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