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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Received on Thu Apr 09 2015 - 09:30:02 PDT
