AMBER Archive (2009)

Subject: Re: [AMBER] Right force fields

From: Patrick Schopf (schopf.patrick_at_googlemail.com)
Date: Fri Apr 17 2009 - 08:34:04 CDT

You would use gaussian or gamess to calulate the mep and then
antechamber or resp to calculate your resp charges. So the answer is
that you will need both programs in any case.

First of all you should read either : Advanced amber tutorials
explaining this procedure in great detail (contains a dye I think but
can't remember the url so just look on the amber homepage) and RED tools
documentation, a collection of perl scripts that try to automate RESP
charge calculations for you, free of charge for academics.

Hope that helps

Patrick

Vikas Sharma wrote:
> Thank you..
>
> Just wanted to know that if am using antechamber for the ligand do i need to do QM calculations using gaussian coz i found one of the tutorials mrntioning use of gaussian for calculation of charges..or is it so thet when i face problems with antechamber then i should go for gaussian
>
>
>
>
> ________________________________
> From: Patrick Schopf <schopf.patrick_at_googlemail.com>
> To: AMBER Mailing List <amber_at_ambermd.org>
> Sent: Friday, 17 April, 2009 6:18:14 PM
> Subject: Re: [AMBER] Right force fields
>
> Hi Vikas,
>
> I can't remember having seen a publication that actually shows
> that ff03 and gaff are 'compatible' in terms of charges.
>
> As long as this has not been published I would not use ff03.
>
> However, this is just an opinion, and not the final experts one.
>
> Patrick
>
>
>
> Vikas Sharma wrote:
>
>>
>> Dear All,
>> I use xleap.
>> The force fields which I use are gaff & ff03..
>> I am working on MM PBSA.
>>
>> Am i Using the right combination of force fields?
>>
>> I just wanted to know that while running antechamber which charges(RESP or BCC) should i use with which force fields?
>>
>> Thanks
>>
>>
>>
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