On Tue, Oct 4, 2011 at 2:06 PM, Sangita Kachhap <sangita.imtech.res.in>wrote:
>
> Thanks Jason for reply
> Actualy when I plot rmsd graph it is not deviating after 8ns it is almost
> stable
> after 10ns so I have taken only 10ns.
>
> I have used only 100 frame for nmode calculation.
>
> shell I have decrease nminterval nminterval=20
> i.e.
> nmstartframe=1, nmendframe=20000,
> nminterval=20
>
> Now the total farme will be used for calculation is 2000.
>
That's a lot and will take a large amount of time. I don't think you'll see
any difference if you increase your nminterval to 100 and only use 200
frames (the above parameters will only calculate 1000 frames though, not
2000).
HTH,
Jason
> Will it be ok?
>
>
>
>
>
> > On Tue, Oct 4, 2011 at 1:14 PM, Sangita Kachhap <sangita.imtech.res.in
> >wrote:
> >
> >>
> >> Hello all
> >>
> >> I am doing MMPBSA analysis for protein-DNA complex. I have 4 trajectory
> of
> >> 5ns
> >> each and I have catenate them to 20ns trajectory.
> >> I have done hydrogen bond analysis of complete 20ns trajectory but
> binding
> >> free
> >> energy calculation of only 10ns.
> >>
> >> Will it affect my result if I compare my 20ns hydrgen bond analysis with
> >> 10ns
> >> calculated bindg free enrgy?
> >> Or should I use complete 20ns trajectory for binding free energy
> >> calculation.
> >>
> >
> > Why not do MMPBSA analysis on your whole trajectory, but only pick out
> every
> > other snapshot? I think it's important to make sure that the
> conformations
> > used to generate the H-bonding data are represented in the FE
> calculations
> > (which isn't guaranteed if you use your approach mentioned above).
>
> >
> >
> >>
> >> One more thing I have used nminterval=100, is it too lagre?
> >>
> >
> > How many frames did you calculate normal modes for? That's the real
> > metric. nminterval=100 is probably too large for 10 frames, but probably
> > sufficient for something like 5000-10000 or something.
> >
> > HTH,
> > Jason
> >
> >
> >> since nmode calculation is time taking so I have used this large value
> of
> >> nminterval.
> >>
> >>
> >>
> >>
> >> With regards
> >>
> >> Sangita Kachhap
> >> JRF
> >> BIC,IMTECH
> >> CHANDIGARH
> >>
> >>
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 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. Candidate
352-392-4032
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Received on Tue Oct 04 2011 - 12:00:02 PDT
