Catherine,
I believe this depends on how your simulations were run and which module you
used.
If you are doing umbrella sampling:
Both the ncsu and nmropt modules produce time series files similar to the
first type you describe. You would probably have to write a simple script
to produce the second file, assuming you used a simple analytic biasing
potential (e.g. harmonic).
If you are doing something else (e.g. REMD):
You would have to calculate the order parameter of interest using ptraj or
some other analysis program (I'm personally more used to VMD). As for the
energy, it would probably have to be recalculated from your trajectory.
I've never actually done this personally, but I believe there is an
established AMBER protocol for it (check the manual, this may also only be
in very recent AMBER releases).
Hope that answers your question,
Brian
On Wed, Sep 14, 2011 at 9:37 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear All,
> I am trying to use MBAR to calculate the PMF energy profile.
> I found in order to run MBAR, we need to input two columns.
> One file contains:. xaxis label "Time (ps)"
> . yaxis label "Angle (degrees)"
>
> Another file contains:. xaxis label "Time (ps)".
> yaxis label "E (kJ
> mol\S-1\N)"
>
> Could you mind to let me know how can we use AMBER to generate those input
> files for MBAR analysis?
> Best regards,
> Catherine
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Wed Sep 14 2011 - 07:30:03 PDT
