Hi Bill,
I am printing below first four steps of min.out.[1]
It is always N (ATOM ID=1) for the rest of the file except the first step where it is O1(ATOM ID= 18).
[1]
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 9.2217E+09 O1 18
BOND = 13750.1241 ANGLE = 10976.5308 DIHED = 2934.9414
VDWAALS = NaN EEL = Infinity EGB = 60228.2741
1-4 VDW = 381037.7111 1-4 EEL = 14860.5376 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
3 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
4 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
5 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
6 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 607581.2350 DIHED = 2262.8000
VDWAALS = 0.0000 EEL = 0.0000 EGB = -2653355.7457
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
——
Jatin Kashyap
Ph.D. Student
Dr. Dibakar Datta Group
Department of Mechanical and Industrial Engineering
New Jersey Institute of Technology (NJIT)
University Heights
Newark, NJ 07102-1982
Phone- (201)889-5783
Email- jk435.njit.edu
> On Jan 5, 2021, at 10:45 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> Here it looks like atom 18 isn't being flagged.
>
> The atom with max gradient is printed at each step. Maybe having the top
> two atoms would help, or any atom with a big diff from the rest should
> also be printed?
>
> Bill
>
>
> On 1/5/21 7:18 PM, Jatin Kashyap wrote:
>> Hi Dave,
>>
>> I just ran it and it gives the below output[1].
>> Can you please help me to interpret it further and what options shall I have in this case.
>>
>> [1]
>> <++>-----------------------------------------------------------------------<++>
>> <++> mdgx: A molecular dynamics engine in the AMBER suite of programs <++>
>> <++> <++>
>> <++> Written by David S. Cerutti, Case Group (2009) <++>
>> <++>-----------------------------------------------------------------------<++>
>>
>> Run on Tue Jan 5 22:03:15 2021
>> <++>-----------------------------------------------------------------------<++>
>>
>> INPUT LINE TEXT:
>>
>> mdgx -i conf_samp.in
>>
>>
>> INPUT FILE TEXT:
>>
>> &files
>> -p complex_NoH.prmtop
>> -c complex_NoH.rst7
>> -o LookAtThis.out
>> &end
>>
>> &configs
>>
>> % General minimization instructions
>> count = 1,
>> verbose 1,
>> maxcyc = 0,
>> strainlim = 20.0,
>> bstrain = 10.0,
>> astrain = 10.0,
>>
>> % Output controls
>> outbase 'Conf', 'Conf',
>> write 'cdf', 'pdb',
>> outsuff 'cdf', 'pdb',
>> &end
>> <++>-----------------------------------------------------------------------<++>
>>
>> <++>-----------------------------------------------------------------------<++>
>> (1.) Energies of the initial and final states. Units are kcal/mol. A number
>> of statistics could be of interest here: this table tries to anticipate
>> them.
>>
>> Statistic Mean Value Std. Dev. Min. Value Max. Value
>> (kcal/mol) (kcal/mol) (kcal/mol) (kcal/mol)
>> ------------------------ ------------ ------------ ------------ ——————
>> Initial E(Model) (a) -0.0000 0.0000 -0.0000 -0.0000
>> Initial E(Restraint) (b) 0.0000 0.0000 0.0000 0.0000
>> Final E(Model) (c) -0.0000 0.0000 -0.0000 -0.0000
>> Final E(Restraint) (d) 0.0000 0.0000 0.0000 0.0000
>> Delta E(Model) (e) -0.0000 0.0000 -0.0000 -0.0000
>> Delta E(Restraint) (f) 0.0000 0.0000 0.0000 0.0000
>>
>> (a) The energies of the initial models, without the restraint energy (this
>> is an indicator of how strained the configurations were before mdgx
>> began to manipulate them).
>> (b) When restraints were first applied to the initial models, these were the
>> restraint energies.
>> (c) The energies of the final models, again excluding restraint energy.
>> This is an indicator of how strained the molecular configurations became
>> after manipulation.
>> (d) Restraint energy needed to get the final configurations into place.
>> (e) This is an indicator of the change in molecular mechanics energy.
>> E(model) will typically rise, indicating that structures became
>> distorted in response to pressure from external restraints.
>> (f) The change in restraint energy. E(restraint) will typically fall as
>> restraints force the structures into new configurations.
>> <++>-----------------------------------------------------------------------<++>
>>
>> <++>-----------------------------------------------------------------------<++>
>> (2.) Convergence statistics for the run. This block of information describes
>> the energy minimization of ALL configurations, regardless of whether they
>> were printed. The next section presents counts of configurations passing
>> the basic sanity checks.
>>
>> - Average steps to convergence: -2147483648 +/- 0
>> - Total converged configurations: 0
>> - Unconverged configurations: 1
>>
>> - Average of the maximal residual force
>> on NON-converged configurations: 0.000000e+00 kcal/mol-A
>> <++>-----------------------------------------------------------------------<++>
>>
>> <++>-----------------------------------------------------------------------<++>
>> (3.) Basic sanity checks. If a configuration fails these tests, it was not
>> printed out for further consideration but the reasons it failed will be
>> summarized here. The tests are that, first, no bond of a configuration
>> may be strained more than 10.00 kcal/mol. Furthermore, no angle may be
>> strained more than 10.00 kcal/mol. Finally, the maximum tolerated
>> restraint energy (summed over all restraints) is 20.00 kcal/mol. If any
>> of these tests seem too stringent or not tight enough, the thresholds may
>> be changed in the &configs namelist.
>>
>> - Configurations passing all sanity checks: 0
>> - Configurations failing bond sanity check: 1
>> - Configurations failing angle sanity check: 1
>> - Configurations failing restraint sanity check: 0
>>
>> Descriptions of each problematic configuration follow, along with the
>> names and numbers of atoms involved in each feature creating the problem.
>> - Configuration 1:
>> Strain is 5150.2037 for bond N -C1 (1, 5)
>> Strain is 251.2722 for angle N -C5 -C4 (1, 9, 8)
>> Restraint binding atoms () strained to 0.0000
>> <++>-----------------------------------------------------------------------<++>
>>
>>
>>
>> ——
>> Jatin Kashyap
>> Ph.D. Student
>> Dr. Dibakar Datta Group
>> Department of Mechanical and Industrial Engineering
>> New Jersey Institute of Technology (NJIT)
>> University Heights
>> Newark, NJ 07102-1982
>> Phone- (201)889-5783
>> Email- jk435.njit.edu
>>
>>> On Jan 5, 2021, at 8:29 PM, David Cerutti <dscerutti.gmail.com> wrote:
>>>
>>> It looks like two of your atoms are somehow overlapping, which may not be
>>> obvious from a visual inspection of a complex system. One clue is the
>>> maximum force you are seeing--it identifies an atom experiencing great
>>> strain. You could check that. Alternatively, you could try loading your
>>> system into mdgx and running a "configuration sampling" of a single
>>> conformation. The input would look something like this:
>>>
>>> &files
>>> -p YourTopology
>>> -c YourInpcrd
>>> -o LookAtThis.out
>>> &end
>>>
>>> &configs
>>>
>>> % General minimization instructions
>>> count = 1,
>>> verbose 1,
>>> maxcyc = 0,
>>> strainlim = 20.0,
>>> bstrain = 10.0,
>>> astrain = 10.0,
>>>
>>> % Output controls
>>> outbase 'Conf', 'Conf',
>>> write 'cdf', 'pdb',
>>> outsuff 'cdf', 'pdb',
>>> &end
>>>
>>> The point is to run one evaluation of the energy (maxcyc = 0 I think will
>>> do it) and then let the routines for checking strain between any given pair
>>> of atoms go to work and tell you where the strain lies. There will be some
>>> detail printed in LookAtThis.out afterwards, although this will be an
>>> all-to-all pair calculation and therefore may take some time to run. I
>>> have used this strategy in the past to elucidate what region of my system
>>> is to blame when minimization fails.
>>>
>>> The more general purpose of these features is to minimize hundreds of
>>> copies of a SMALL molecule at the same time, all subject to different
>>> restraints to make their conformations diverge, and then analyze any
>>> results that failed to reach a local energy minimum without great strain in
>>> some bond, angle, or overall restraint energy. It will give somewhat more
>>> detailed explanations of these failed systems than the imin=1 diagnostics
>>> in a sander mdout, so that the user can then tailor the restraints or add
>>> other minimization attempts to improve the success rate and ultimately get
>>> a large set of energy-minimized conformations which are geometrically
>>> distinct but all reasonably relaxed.
>>>
>>> Dave
>>>
>>>
>>> On Tue, Jan 5, 2021 at 7:55 PM Jatin Kashyap <jk435.njit.edu> wrote:
>>>
>>>> Dear AMBER Community,
>>>>
>>>> I am getting an error[1] upon performing minimization of drug-protein
>>>> complex by using the AMBER tutorial[2].
>>>> There seems to be nothing wrong with the complex as per visual inspection
>>>> of complex PDB file obtained after parametrization.
>>>> Please let me know if sharing the output file can be more helpful.
>>>>
>>>> Thank you very much.
>>>>
>>>> [1]
>>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>>> 1 NaN NaN 9.2217E+09 O1 18
>>>>
>>>> BOND = 13750.1241 ANGLE = 10976.5308 DIHED =
>>>> 2934.9414
>>>> VDWAALS = NaN EEL = Infinity EGB =
>>>> 60228.2741
>>>> 1-4 VDW = 381037.7111 1-4 EEL = 14860.5376 RESTRAINT =
>>>> 0.0000
>>>> .
>>>> .
>>>> .
>>>> .
>>>> .
>>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>>> 2519 NaN NaN 0.0000E+00 N 1
>>>>
>>>> BOND = NaN ANGLE = 607581.2350 DIHED =
>>>> 2262.8000
>>>> VDWAALS = 0.0000 EEL = 0.0000 EGB =
>>>> -2653355.7457
>>>> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
>>>> 0.0000
>>>>
>>>>
>>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>>> 2520 NaN NaN 0.0000E+00 N 1
>>>>
>>>> BOND = NaN ANGLE = 607581.2350 DIHED =
>>>> 2262.8000
>>>> VDWAALS = 0.0000 EEL = 0.0000 EGB =
>>>> -2653355.7457
>>>> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
>>>> 0.0000
>>>>
>>>>
>>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>>> 2521 NaN NaN 0.0000E+00 N 1
>>>>
>>>> BOND = NaN ANGLE = 607581.2350 DIHED =
>>>> 2262.8000
>>>> VDWAALS = 0.0000 EEL = 0.0000 EGB =
>>>> -2653355.7457
>>>> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
>>>> 0.0000
>>>>
>>>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>>>
>>>> ***** REPEATED LINMIN FAILURE *****
>>>>
>>>> ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO
>>>> *****
>>>>
>>>>
>>>> FINAL RESULTS
>>>>
>>>>
>>>>
>>>> NSTEP ENERGY RMS GMAX NAME NUMBER
>>>> 2521 NaN NaN 0.0000E+00 N 1
>>>>
>>>> BOND = NaN ANGLE = 607581.2350 DIHED =
>>>> 2262.8000
>>>> VDWAALS = 0.0000 EEL = 0.0000 EGB =
>>>> -2653355.7457
>>>> 1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT =
>>>> 0.0000
>>>>
>>>>
>>>> [2]
>>>> https://ambermd.org/tutorials/basic/tutorial4b/index.php
>>>>
>>>> ——
>>>> Jatin Kashyap
>>>> Ph.D. Student
>>>> Department of Mechanical and Industrial Engineering
>>>> New Jersey Institute of Technology (NJIT)
>>>> University Heights
>>>> Newark, NJ 07102-1982
>>>> Phone- (201)889-5783
>>>> Email- jk435.njit.edu
>>>>
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Received on Tue Jan 05 2021 - 20:00:03 PST
