2011/5/9 geyan <geyan.big.ac.cn>
> It's really hard for me to accept the fact that I have to start from
> beginning as I have spent 6 whole days to get the "snapshot_com.all.out" and
> "snapshot_rec.all.out" with just some little problems in
> "snapshot_lig.all.out" which I think maybe due to the programme itself.
Do you have an error message to support this suspicion?
> Since my computation power here is not so strong, it's very frustrated for
> me to start all the computation from the first snapshot. Is there really no
> any method to make use of the already produced results to continue
> calculation?
>
Without hacking it, no. mm_pbsa.pl will go through each snapshot and
calculate the energy, then extract the information from each file. If you
understand how each of the steps of the calculation are done, then what you
can do is finish the rest of the calculations for the ligand by hand, then
collect the statistics at the end.
Of course the above is vague since I've never hacked on mm_pbsa.pl (that
would've required me to learn perl, and I'm content with Python), so you'll
have to do most of the work to figure out how to implement the guidelines I
specified by yourself.
Here I guess it's just a question of what is more costly -- 6 days to rerun
your calculation (I would do only a couple snapshots just to make sure it
works, first! 4000 snapshots seems like significant overkill to me for most
tasks), or find out how to hack mm_pbsa.pl to find out how to make use of
the computer time already spent on it.
I would also suggest trying MMPBSA.py included with AmberTools 1.5, since it
should probably be a little faster and runs in parallel with good scaling
(it is also easier to use and catches errors more easily). Perhaps the
biggest reason, though, is because the people on the list that respond to
MM/PBSA questions are far more versed in the Python version than the Perl
one, so you'll get more (better) help with that one.
HTH,
Jason
Best regards!
>
> 2011-05-09
>
>
>
> geyan
>
>
>
> 发件人： Bill Miller III
> 发送时间： 2011-05-09 22:43:46
> 收件人： AMBER Mailing List
> 抄送：
> 主题： Re: [AMBER] How to restart the MM-PBSA?
> There is no real way to restart the mm_pbsa.pl calculation. Of course, if
> you have already generated the snapshots, you won't have to do that again.
> But the calculation itself will need to be restarted from the beginning.
> -Bill
> On Sun, May 8, 2011 at 9:16 AM, geyan <geyan.big.ac.cn> wrote:
> > Dear all Amber friends,
> > I met a problem in calculating the MM-PBSA. I have 4000 snapshots in
> > total, but when I use the "mm_pbsa.pl" script to calculate the binding
> > energy, I met some mistakes in the final period. Now my question is how
> can
> > I restart the calculation from the stop point, that is not recalculate
> from
> > stratch.
> >
> > 2011-05-08
> >
> >
> >
> > geyan
> > _______________________________________________
> > 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
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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 Mon May 09 2011 - 09:00:02 PDT
