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 - 19:30:03 PST
