Oh yes it will calculate 1000 not 2000 frames.
> 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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>> >>
>> >
>> >
>> >
>> > --
>> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Oct 04 2011 - 21:30:02 PDT
