Dear Jason,
That helped a lot, actually. I was missing something important, which was
the
pmemd input parameter that tells me how many frames it writes down on the
mdcrd files. That was pretty dumb, I know, but thanks to your tip (and some
patience),
I was able to nail the problem down. Thank you very much!
Gabriel
2011/4/27 Bill Miller III <brmilleriii.gmail.com>
> Without seeing your input file, I can only guess at your problem. However,
> I
> assume the issue is that you are assuming MMPBSA.py is reading all your
> trajectories as a single trajectory and using that for the start, end, and
> interval variables. However, these variables are for each trajectory, not
> for all the trajectories in their entirety. For example, if you have 20
> trajectories with 1000 frames each and you set start=50, end=100,
> interval=2, it will take every other frame starting at frame 50 and ending
> at 100 for *each* trajectory. So instead of having only 25 frames, you
> would
> actually have 25 frames x 20 trajectories = 500 frames analyzed.
>
> My guess is that you have 200 frames or less in each of your trajectories,
> which gets MMPBSA.py confused because then it is trying to take from frames
> that do not exist when you tell it to start at frame 200 for each
> trajectory. So you can either 1) use ptraj to combine all your trajectories
> into a single trajectory before running MMPBSA.py or 2) you can use
> start,end, interval in a way that better matches what you want.
>
> I hope that helps.
>
> -Bill
>
> On Wed, Apr 27, 2011 at 7:52 AM, Gabriel Urquiza <urquizagabes.gmail.com
> >wrote:
>
> > Dear Amberists,
> >
> > I've been having some hard times making MMPBSA.py understand what is it
> > that
> > I want to do.
> > I'm using it to estimate binding free energy between an enzyme and a
> > ligand,
> > pretty standard
> > stuff. In order to do so, I am using several trajectories in the
> > expectation
> > that by doing so I
> > will better sample phase space and therefore will obtain more
> statistically
> > meaningful results.
> >
> > However, when I tell MMPBSA.py that I want it to cut through the
> > trajectories from frame 200
> > to frame 20000 it will tell me this:
> >
> > WARNING in safe_close(): Attempting to close a NULL FILE and buffer!
> >
> > Beginning quasi-harmonic entropy calculation with ptraj...
> > Error! Ptraj failed. Check coordinate and topology files for the complex.
> >
> > And when I start from frame 1 to frame 20000 it will go on and give me my
> > calculations, except
> > that it will take a single frame from each trajectory. Does anyone have a
> > clue of what on earth is
> > going on here? At first I thought it was something to do with the
> > trajectories being too short, maybe
> > a bug. But the interval is valid for all trajectories.
> >
> > Looking forward to your assistance.
> >
> > Gabriel
> >
> > ---------
> > Graduation student at Federal University of Paraíba, Brazil.
> > LQQC - Laboratory of Computational Quantum Chemistry
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 27 2011 - 06:30:10 PDT
