AMBER Archive (2009)

Subject: Re: [AMBER] Amber Sulfate Ion Parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Apr 23 2009 - 01:07:40 CDT


Hi Neha,

> I tried using the same parameters for sulphate but my paper got
> rejected saying these parameters are too old. The reviewers introduced
> me to new parameters which others have referred from Lan Jin thesis,
> University of edinburgh. There is no ppublication out there about the
> parameters, but you might contact Dusan Uhrin at university of
> edinburgh. These parameters can be used with amber or glycam
> forcefields.

ok thanks for letting us know...

regards, Francois

>>> I am trying to find parameters for the sulfate ion in Amber. I have only
>>> found the parameter set of Huige & Altona (1995) for this ion, however,
>>> only
>>> the bond and angle parameters are stated.
>>
>> Yes, you are right; these are the parameters used for this ion.
>>
>>> I am not sure what nonbonded
>>> parameters they use. Would it be okay to use
>>>
>>> OS          1.6837  0.1700             OPLS ether
>>> S           2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
>>
>> Yes
>>
>>> from parm99? Alternatively, is anybody aware of any other sulfate ion
>>> parameter sets?
>>
>> I do not think so.
>>
>> regards, Francois
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Regards,
> Neha Gandhi,
> School of Biomedical Sciences,
> Curtin University of Technology,
> GPO Box U1987 Perth,
> Western Australia 6845
>
>

           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber