Dear Prof. Fyd,
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).
regards;
________________________________
From: FyD <fyd.q4md-forcefieldtools.org>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Saturday, July 14, 2012 2:45 PM
Subject: Re: [AMBER] benzene-sulfonate (atom type for Sulfur)
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
