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.
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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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Oct 04 2011 - 11:30:03 PDT
