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
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AMBER mailing list
AMBER.ambermd.org
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Received on Mon Feb 07 2011 - 08:30:02 PST
