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
Received on Mon Feb 07 2011 - 10:30:09 PST
