Sofia,
Line minimizer aborted: step at upper bound 0.11052506
> Line minimizer aborted: step at upper bound 0.0018891926
> Line minimizer aborted: (brackt && (stp<=MIN(stx,sty) ||
>
That more or less looks like it's stuck on minimization, though I've never
seen the last line before. Of course, your system might be fairly large for
nmode, so it's also possible that the size is interfering with MMPBSA from
finding a good minimum- I've only ever tried with systems a lot smaller
than yours, so that's purely conjecture.
I've glanced through the mailing list archives, but there doesn't seem to a
go to fix for it besides trying to minimize your systems further before
running nmode- this thread (
http://archive.ambermd.org/201401/0085.html)
might give you some ideas of how you might do it, ie run production for a
longer time, or use sander/imin=5 as suggested.
Best,
Kenneth
On Fri, Apr 10, 2015 at 6:23 PM, Sofia Vasilakaki <svasilak.chem.uoa.gr>
wrote:
> Thank you for your reply,
>
> I have tried use_sander=1 using 4 frames but I got the same error. I have
> boundary conditions and this may cause problems (although I have run nmode
> in other proteins with periodic boundaries and there was no problem) so Ι
> used cpptraj and nobox to built prmtops but no results. My system is
> 132,866 atoms.
>
> Now I m running nmode in one frame (MMPBSA.py) and gb=0 and so far
> (12hours) I am getting this in progress. log
>
> Line minimizer aborted: step at upper bound 0.11052506
> Line minimizer aborted: step at upper bound 0.0018891926
> Line minimizer aborted: (brackt && (stp<=MIN(stx,sty) ||
> stp>=MAX(stx,sty))) || (dx * (stp-stx) >= 0) || stpmax < stpmin
> brackt = 0
> stp = 1
> stx = 0
> sty = 0
> stpmin = 0
> stpmax = 5
> dx = 0.00117415
>
>
> Thank you,
> Sofia V.
>
>
> > Sofia,
> >
> > Huh. From your description, I'm going to guess that one of two things are
> > going on- either MMPBSA is running into a problem somewhere else and the
> > message is getting swallowed up, or MMPBSA can't find a way to get your
> > system to a lower energy state.
> >
> > In the first case, you can try adding in use_sander=1 to the input; I've
> > never used it in conjunction with nmode before, so I have no idea how
> well
> > it meshes or if it'll actually provide any information. You can also try
> > running a smaller set of frames, ie one or two, to see if it'll crash
> with
> > the same issue. It's fully possible your system is very large for nmode,
> > and MMPBSA is running out of memory as nmode gets very, very expensive
> > with
> > larger systems.
> >
> > But if it is actually stuck on minimization, I have honestly no idea how
> > you'd fix it. It'd basically mean that nmode is trying to minimize one or
> > more of your frames, and is unable to find a way in one or more frames so
> > ends up getting stuck; there might be a solution in the mailing list
> > somewhere, or a developer might want to weigh in.
> >
> > Also, looking back at your error message- does your system have periodic
> > boundaries? If so, it might be worth looking into, since I don't think
> > nmode plays well with those.
> >
> > Best,
> >
> > Kenneth
> >
> > On Thursday, April 9, 2015, Sofia Vasilakaki <svasilak.chem.uoa.gr>
> wrote:
> >
> >> Hi again,
> >>
> >> So yes, I had increased maxcyc to 15000 without any difference ...
> >> The _MMPBSA_complex_nm.out files have endless steps of min like the one
> >> that follows. It is trying to do "something" but since I do not know how
> >> mpbsa_entropy.nab works (could not understand the script either) I can
> >> not
> >> figure out what is looking for or what cause the min process to fail.
> >>
> >>
> >> MIN: Iter = 1011 NFunc = 8109 E = -20202.40567 RMSG =
> >> 3.0950510e-03
> >> CG: It= 5 ( 0.404)q :-)
> >> LS: i= 1 lhs_f= -0.00064243311 rhs_f= -1.4486479e-07
> >> lhs_g= 0.00013928903 rhs_g= 0.0013037831
> >> rel_s= 1 abs_s= 0.0091621209
> >> max_d= 0.0022346375 i_xyz= 1321z
> >> LS: step= 1 it= 1
> >> MIN: Iter = 1012 NFunc = 8115 E = -20202.40633 RMSG =
> >> 2.4451938e-03
> >> CG: It= 50 ( 3.946)q :-(
> >> LS: i= 1 lhs_f= 0.090179125 rhs_f= -2.5904682e-06
> >> lhs_g= 0.28272781 rhs_g= 0.023314214
> >> rel_s= 1 abs_s= 0.490173
> >> max_d= 0.11656831 i_xyz= 1321z
> >> LS: i= 2 lhs_f= -0.0022555352 rhs_f= -4.10196e-07
> >> lhs_g= 0.0012501516 rhs_g= 0.023314214
> >> rel_s= 0.15834821 abs_s= 0.077618017
> >> max_d= 0.018458384 i_xyz= 1321z
> >> LS: step= 0.15834821 it= 2
> >>
> >>
> >>
> >> > Sofia,
> >> >
> >> > Line minimizer aborted: max number of iterations reached
> >> >
> >> >
> >> > I think this might be your primary issue. I'm assuming that the error
> >> > message means the same thing as it would in other programs, so in this
> >> > case
> >> > it'd mean that MMPBSA is hitting the maximum number of times it can
> >> try
> >> to
> >> > use- reading through the manual, I'd venture to guess that maxcyc is
> >> the
> >> > value you'd want to look at increasing?
> >> >
> >> > As a good way to double check, have you checked what the mdout file
> >> says?
> >> >
> >> > Though, I've never seen this error before in relation to Amber, and
> >> have
> >> > very limited experience with nmode, so someone else might want to
> >> weigh
> >> > in.
> >> >
> >> > Best,
> >> >
> >> > Kenneth
> >> >
> >> > On Thu, Apr 9, 2015 at 10:39 AM, Sofia Vasilakaki
> >> <svasilak.chem.uoa.gr>
> >> > wrote:
> >> >
> >> >> Hello to everyone!
> >> >>
> >> >> So, I am trying to run MMPBSA.py.MPI for nmode and the calculation
> >> for
> >> >> _MMPBSA_complex_nm.out gets stack in minimazition. The error I
> >> receive
> >> >> in
> >> >> progress . log (between endless lines of Line minimizer aborted ...)
> >> is
> >> >>
> >> >> Line minimizer aborted: max number of iterations reached
> >> >> Line minimizer aborted: rounding error
> >> >> Second derivatives are not supported for periodic systems; exiting.
> >> >> File "/opt/amber14/bin/MMPBSA.py.MPI", line 96, in <module>
> >> >> app.run_mmpbsa()
> >> >> File "/opt/amber14/bin/MMPBSA_mods/main.py", line 218, in
> >> run_mmpbsa
> >> >> self.calc_list.run(rank, self.stdout)
> >> >> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
> >> >> calc.run(rank, stdout=stdout, stderr=stderr)
> >> >> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 309, in
> >> run
> >> >> Calculation.run(self, rank, stdout=self.output % rank)
> >> >> File "/opt/amber14/bin/MMPBSA_mods/calculation.py", line 148, in
> >> run
> >> >> self.prmtop))
> >> >> CalcError: /opt/amber14/bin/mmpbsa_py_nabnmode failed with prmtop
> >> >> Com.prmtop!
> >> >> Error occured on rank 3.
> >> >> Exiting. All files have been retained.
> >> >> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
> >> >> Line minimizer aborted: max number of iterations reached
> >> >>
> >> >>
> >> >> I have try many different ways of setting up the process (such as:
> >> use
> >> >> same protein but different ligands in amber12 & amber 14, gb=0 or 1,
> >> >> ways
> >> >> of producing prmtops ... ) but always the same error. So, should I
> >> try
> >> >> mm_pbsa instead? Has to do with the protein ? With the system ? Any
> >> >> other
> >> >> ways for estimating entropy ?
> >> >>
> >> >> Thank you in advance,
> >> >> Sofia V.
> >> >>
> >> >>
> >> >> _______________________________________________
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> >> >> AMBER.ambermd.org
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> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Ask yourselves, all of you, what power would hell have if those
> >> imprisoned
> >> > here could not dream of heaven?
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> >> >
> >>
> >>
> >>
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>
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Received on Sat Apr 11 2015 - 16:00:05 PDT
