On Sat, Jun 19, 2010 at 4:30 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Here I am minimizating first Hydrogen only because of all the close contact
> are
> due to added Hydrogen by leap.
>
But you should also allow the sidechains to move out of the way, since only
moving hydrogens won't do much good, I don't think. Again, I advise that
you just restrain the backbone atoms, and let the hydrogens and sidechains
alike do as they will.
Good luck!
Jason
>
>
>
> > Hello,
> >
> > On Sat, Jun 19, 2010 at 3:59 PM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >> Ya I have seen the tutorial for simulation of DNA in implicit solvant
> >
> >
> > There is no tutorial for "constant pH" simulations specifically, though
> it
> > is not much different than other implicit solvent simulations
> >
> >
> >> there is relaxing the DNA before MD simulation at tempi = 300.0, temp0 =
> >> 300.0.
> >> But actualy in one of the reply of my mail I got about heating and
> >> equilibration
> >> so thats why I have confusion.
> >> For constant pH simulation I am donig the following step is it correct
> or
> >> not?
> >> 1)minimization:
> >> a)minimization of hydrogen only (by mistake I my earlier mail I have
> wrote
> >> that i hvae apply restraint on hydrogen).
> >>
> >
> > I would not minimize just the hydrogens. The hydrogen distances won't
> > change due to SHAKE, so I don't think you gain much by this step.
> >
> >
> >> b)minimization of whole system
> >>
> >
> > This seems to me to be the only minimization you really need. It doesn't
> > need to be long, either, since it's just relaxing bad contacts. You may
> > also add restraints to the backbone atoms to prevent any kind of major
> > distortion of secondary structure.
> >
> >
> >>
> >> 2)heating (now which I will not do) and equilibration at tempi = 300.0,
> >> temp0 =
> >> 300.0
> >>
> >
> > You certainly need to heat. And apply restraints to the backbone atoms
> like
> > I've suggested, most likely. I have, on occasion, seen the entire
> protein
> > unravel during heating, though that could be due to a couple bugs that
> were
> > patched up in the constant pH code (make sure you apply all of these bug
> > fixes! 47 for amber9 and 25 for amber10). In any case, I think it's a
> good
> > idea to apply some restraints to the backbone while you're heating and
> > equilibrating.
> >
> >
> >>
> >> 3)production run.
> >>
> >
> > You can take off all restraints here and just run freely.
> >
> >
> > Good luck!
> > Jason
> >
> >
> >>
> >> >> Now I have to euqilibrat it with heating 0 - 300K.
> >> >
> >> > Have you looked at the tutorials?
> >> >
> >> > Bill
> >> >
> >> > _______________________________________________
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> >> > 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
> 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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Received on Sat Jun 19 2010 - 14:30:04 PDT
