AMBER Archive (2006)

Subject: Re: AMBER: TI, mutation

From: eric.henon_at_univ-reims.fr
Date: Tue Aug 29 2006 - 03:43:04 CDT

Thank you to Pradipta and Carlos
for their response.
E. Henon

Pradipta Bandyopadhyay:

>
> In your thermodynamic cycle, energy contributions coming from bond, angle
> parameters of dummy atoms will cancel out.
>
> Pradipta

Carlos Simmerling:

have you worked through the Amber tutorial on using TI?
even though it's not for ligand binding you should do it
first and then see if there are things that still are unclear.

>
> On Mon, 28 Aug 2006 eric.henon_at_univ-reims.fr wrote:
>
>> Hello,
>> I'm a new Amber's user (version 7) and
>> I want to calculate free energy changes
>> with sander TI
>> (more precisely a relative binding free energy
>> using a thermodynamic cycle).
>>
>> I understood it is
>> needed to create a "frcmod" file that gives the properties of
>> the dummy atoms,
>> when certain atoms disappear from the initial state.
>>
>> All the examples I found on the list give
>> as I expected it, zero vdw parameters in this case, but
>> bond and angle parameters that correspond to
>> "real" atoms ... (non-zero mass and non-zero force constants ?!).
>> This will add potential
>> energy terms which have no signification for
>> the desired final state ... (? )
>>
>> Any comments will be appreciated.
>> Thank you in advance.
>>
>>
>> E. Henon
>>
>>
>>
>>
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