Thanks Jason for reply
Here I am not fully understood what have you told.
What I understood is
I have a trajectory of production run that is ready for MMPBSA.
As my first experiment is to calculate binding energy of the protein - DNA complex
without the water molecule (which effect in binding energy I have to measure)
So after production run I will go for MMPBSA normaly without any specification
using .prmtop (implicit solvent (water))
Now for second experiment claculate binding energy in presence of that water
molecule.
Again I have the trjectory of protein- DNA - slovent
To calculate binding free energy in presence of that water molecule I have to
strip
all solvent molecule which I dont required for calculation using closest command
Now I have a trajectory of protein - DNA - water
Next I have to go for MMPBSA here I have trajectory but what .prmtop I should
use here?
Since I dont have .prmtop for protein - DNA - water, shuold I have to generate
new PDB
form modify trajectory then generate .prmtop and use this .prmtop to MMPBSA run.
To include the water molecule I can use the command e.g. closestwater 50 :1-20
first
save 50 molecule closest to residues 1-20 then go rfor .prmtop generation and
MMPBSA
Is what I am thinking are right?
Please guide me to understand it.
> Hello,
>
> On Sat, Feb 5, 2011 at 2:13 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> Hello all
>>
>> I want to study the effect of perticular water molecule on affinity and
>> specificity
>> of protien DNA binding.
>> As these can be define by standared free energy change I thought,if I can
>> calculate the
>> standared free energy change of protein - DNA interaction
>>
>> 1)considering that perticular water molecule in interaction
>>
>> 2)In absence of that perticular water molecule
>>
>> Then the effect of water molecule in affinty and specificity can be define.
>> So I thought to use MMPBSA but it runs implicit and I am not getting how to
>> include
>> that perticular water molecule in calculation of standared free energy
>> change.
>>
>> Can anyone please suggest is it possible and how to do it?
>>
>
> You can still use MM/PBSA. If you use MMPBSA.py, you will have to
> preprocess the trajectory and strip out all of the waters that you don't
> want to include (just the one that you do). Check out the "closest" command
> in ptraj. After this, just set "strip_mdcrd = 0" to prevent the script from
> stripping bulk solvent and include the water molecule in either the receptor
> or ligand topology files. Note that MMPBSA still uses an implicit solvent
> model (which I think is what you want), but still treats that one important
> water molecule explicitly.
>
> You can do decomposition analysis to aid in looking at specific
> interactions.
>
> Hope this helps,
> Jason
>
>
>> With regard
>> Sangita Kachhap
>> JRF
>> BIC,IMTECH
>> CHANDIGARH
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 06 2011 - 07:30:04 PST
