Thank you so much Jason
> On Mon, Feb 7, 2011 at 1:20 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
>> 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.
>>
>
> Yes, but you may want to specify a particular atom in your mask, rather than
> an entire residue. Also make sure you visualize the trajectory afterwards
> so you make sure that you keep the water you wanted to keep.
>
> Good luck!
> Jason
>
>
>>
>>
>>
>>
>> > 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
>> 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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http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 07 2011 - 11:30:03 PST
