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
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Ask yourselves, all of you, what power would hell have if those
> imprisoned
> > here could not dream of heaven?
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
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Received on Fri Apr 10 2015 - 10:00:05 PDT
