Dear Prof. Fyd,
>> ~260 or ~250? & what about 255? ;-)
>>use gaff, I think it does not matter; try one and see how you can
>>reproduce experimental data with that...
Antechamber provides s6 atom type, may be antechamber goes crazy sometimes. Yes I need to compare using one of the types.
thanks,
________________________________
From: FyD <fyd.q4md-forcefieldtools.org>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Saturday, July 14, 2012 3:41 PM
Subject: Re: [AMBER] benzene-sulfonate (atom type for Sulfur)
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 - 04:00:03 PDT
