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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--
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 - 11:00:07 PDT
