Thanks you Jason for reply
I have to include only one water molecule which is invole in fomration of H-bond
between DNA and protein I have mention 50 for an example.
If somehow I capture this in trajectory can I use following command to select that
water in protein?
closest 1 :50
i.e. one water molecule close to 50th residue of protein.
> Ah, I thought I had already responded; apparently not. My mistake.
>
> On Mon, Feb 7, 2011 at 10:50 AM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>>
>> 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)
>>
>
> Do you want 50 water molecules? I was under the impression that you only
> wanted 1. The point is that any water molecules that you want to explicitly
> include in the simulation you must somehow capture in a trajectory. I
> simply suggested the "closest" command as that's the first thing that came
> to mind when thinking about this problem.
>
>
>>
>> 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
>>
>
> Yes. You must create a topology file with the waters in them. Think about
> where you want them included in the calculation (ligand or receptor), and
> put them there. If you include them as part of the receptor and your ligand
> residues are continuous, MMPBSA.py should be able to figure out your two
> masks, respectively.
>
> Good luck!
> Jason
>
>
>>
>> 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
>>
>
>
>
> --
> 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
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
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Received on Mon Feb 07 2011 - 10:30:08 PST
