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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>> >>
>> >
>> >
>> >
>> > --
>> > 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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Received on Fri Apr 10 2015 - 15:30:04 PDT
