Then I'd see what the distance is between O1/18 and its connected atoms.
See how GMAX is 0 after step 1 (because the ff terms have escaped the
mathematical universe), so I'll bet atom 1 is the first one checked and
it goes nowhere.
Bill
On 1/5/21 7:53 PM, Jatin Kashyap wrote:
> 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
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
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Received on Tue Jan 05 2021 - 20:00:04 PST
