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

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Sat, 14 Jul 2012 11:15:46 +0200

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 - 02:30:03 PDT
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