Dear Prof. Fyd
>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
thanks,
Jio
________________________________
From: FyD <fyd.q4md-forcefieldtools.org>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Friday, July 13, 2012 9:31 PM
Subject: Re: [AMBER] benzene-sulfonate (atom type for Sulfur)
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 14 2012 - 00:00:02 PDT
