Re: [AMBER] Total interaction energy between monomeric units of a dimer

From: Hector A. Baldoni <hbaldoni.unsl.edu.ar>
Date: Thu, 20 Aug 2015 09:09:43 -0300 (ARGSL-ST)

Hi Anu,

Attached you will find some in/out files about how to calculate the
interaction energies between protein-K+ using anal. You could download
anal software, compile and learn from the attached file how to use it.
I hope this will help you.

Greeting,
Hector.



> Hi,
> Do we have any utility in latest versions of Amber, which do calculations
> what 'anal' did in older versions of Amber?. In other words, is it
> possible
> to do group decomposition of energy in MMPBSA.py, i.e total interaction
> energy between two groups, say group A (residue 1-100) and group B
> (residue
> 200-250) or group A (residue 50 ) and group B (residue 200-250)?. I
> noticed
> that 'anal' does this sort of decomposition of total energy and I wonder
> why Amber has completely removed 'anal' from its 10th version onwards.
>
> Many thanks
> Anu
>
> On Wed, Aug 19, 2015 at 5:22 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Wed, Aug 19, 2015, George Tzotzos wrote:
>> >
>> > Assuming a GB calculation, would it be legitimate to treat one of the
>> > subunits (say subunit A) as a receptor and the other as ligand.
>>
>> Yes: the terms "ligand" and "receptor" are just labels. Any problem
>> that
>> has
>> A + B interacting non-covelently can in principle to addressed by these
>> methods.
>>
>> > Generate
>> > topologies for ligand, receptor and complex using ante-mmpbsa.py and
>> > then run mmpbsa.py to calculate deltaG of subunit B.
>>
>> This gets you the free energy of interaction, not the free energy of
>> interaction "of subunit B". It doesn't matter which subunit you call
>> "ligand"
>> and which one you call "receptor".
>>
>> > Repeat same procedure (using subunit B as receptor) to calculate
>> deltaG
>> of
>> > subunit A. Would adding the deltaGs of the two subunits correspond to
>> > the total interaction energy?
>>
>> There is no need to repeat anything. The two calculations you describe
>> are
>> identical. [If not, them I am not understanding what you are proposing
>> to
>> do.]
>>
>>
>> ....dac
>>
>>
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--------------------------------------
 Dr. Hector A. Baldoni
 Area de Quimica General e Inorganica
 Universidad Nacional de San Luis
 Chacabuco 917 (D5700BWS)
 San Luis - Argentina
 hbaldoni at unsl dot edu dot ar
 Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------

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Received on Thu Aug 20 2015 - 05:30:05 PDT
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