Hello Jason
Sorry for again mailing you.
I have some confusion what you have suggest me in concern to
"measurement of effect of perticular water molecule on affinity and specificity"
As first experiment is to calculate binding energy of the protein - DNA - complex
without the involement of that perticular water molecule in binding energy
calculation
So after production run I will go for MMPBSA normaly without any specification
using implicit.prmtop
Second experiment is to calculate binding energy of the protein - DNA complex
with the involement of that perticular water molecule in binding energy calculation
As you told to do this first strip water molecule from production run trajectory
using closest command
(e.g. closestwater 50 :1-20 first
this will save 50 water molecule closest to residues 1-20)
Then go for MMPBSA here I have a question, should I have to generate another
.prmtop for
protein - DNA - water? since I have .prmtop for only protein - DNA complex not for
perticular water molecule included
Please suggest me.
> 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 07 2011 - 08:00:03 PST
