Dear David, Adrian and all,
While running nmode calculation with 2 frames I'm getting the following
warning messages.
Googling about this error gives an older archive discussion here
<
http://archive.ambermd.org/201703/0308.html>, but the job terminates after
some time without leaving any output file which I can inspect for potential
reasons. At the end are the input and terminal output that I saved to a
file.
Can you please suggest a modification to input or command-line options that
can help me in tracing the problem with this nmode calculation?
Looking forward to your valuable suggestions and insights.
Line minimizer aborted: step at upper bound 0.0037932842
Line minimizer aborted: step at upper bound 0.14410834
Line minimizer aborted: step at upper bound 0.019404514
Line minimizer aborted: step at upper bound 0.0019865013
Line minimizer aborted: step at upper bound 0.015107794
Line minimizer aborted: step at upper bound 0.0012514619
Line minimizer aborted: step at upper bound 0.052486681
Line minimizer aborted: step at upper bound 0.04794522
Line minimizer aborted: step at upper bound 0.0018475019
Line minimizer aborted: step at upper bound 0.0012051239
(base) [exx.c107739 MMPBSA]$ more mmpbsa-nmode.in
Input file for running nmode and GB
&general
endframe=2000, verbose=2, interval=1000,
# entropy=1,
/
&gb
igb=5,
/
&nmode
nmstartframe=1, nmendframe=2000, nminterval=1,
maxcyc=50000, drms=0.0001,
/
(base) [exx.c107739 MMPBSA]$ more mmpbsa-nmode-nf2endfr2000.out
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /usr/local/amber18/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/amber18/bin/cpptraj
mmpbsa_py_nabnmode found! Using /usr/local/amber18/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
2 frames were processed by cpptraj for use in calculation.
2 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning GB calculations with /usr/local/amber18/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning nmode calculations with /usr/local/amber18/bin/mmpbsa_py_nabnmode
calculating complex contribution...
Thank you and best regards
Vaibhav
On Mon, Apr 19, 2021 at 7:49 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Sorry, my mistake, the unit for kb was M-1 (not s-1 which was for kET).
> With this correction, I think it would make sense to use the DG
> relationship with kb.
>
> On Mon, Apr 19, 2021 at 7:45 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
>
>> Hi
>>
>> Just to clarify, kb in units of s^-1 is NOT a measure of affinity. It
>> could be rate constant, but for sure, it is not anything you would want
>> to use to do
>>
>> Delta-G = -RT * ln(kb)
>>
>>
>>
>> Adrian
>>
>>
>> On 4/18/21 1:20 PM, Vaibhav Dixit wrote:
>> > [External Email]
>> >
>> > Dear All,
>> > I'm getting very high entropy values after running the MMPBSA with the
>> > following input.
>> > The vibrational contribution seems very large (-ve) number.
>> > The GBSA based enthalpy looks reasonable since the two proteins are
>> known
>> > to have a weak binding affinity (kb ~ 700 s-1) at 300 K. I was hoping
>> to
>> > combine the Delta-H (from GBSA and PBSA) calculations with Delta-S
>> > calculations to get the total Delta-G and then use Delta-G = -RT *
>> ln(kb)
>> > to see if it agrees with the experimental data.
>> >
>> > Can you please help me understand what might be the problem here?
>> > It will also help if you can comment on the correctness of my approach
>> here
>> > and what might be the associated pitfalls. The MMPBSA reference doesn't
>> > seems to address these aspects.
>> > Thus valuable insights and comments are highly appreciated.
>> > Thanks a lot and best regards.
>> >
>> > | Run on Mon Apr 19 00:34:17 2021
>> > |
>> > |Input file:
>> > |--------------------------------------------------------------
>> > |Input file for running nmode and GB
>> > |&general
>> > | endframe=2000, verbose=2, interval=5,
>> > | entropy=1,
>> > |/
>> > |&gb
>> > | igb=5,
>> > |
>> > |/
>> > |
>> > |--------------------------------------------------------------
>> > |MMPBSA.py Version=14.0
>> > |Solvated complex topology file: ../1hga-3ner-solv.prmtop
>> > |Complex topology file: 1hga-3ner-complex.prmtop
>> > |Receptor topology file: 1hga-recp1.prmtop
>> > |Ligand topology file: 3ner-lig1.prmtop
>> > |Initial mdcrd(s): ../1hga-3ner-solv-prod300-reimaged.nc
>> > |
>> > |Receptor mask: ":1-143"
>> > |Ligand mask: ":144-235"
>> > |
>> > |Calculations performed using 400 complex frames.
>> > |
>> > |Generalized Born ESURF calculated using 'LCPO' surface areas
>> > |
>> > |All units are reported in kcal/mole.
>> > |All entropy results have units kcal/mol (Temperature is 298.15 K).
>> >
>> -------------------------------------------------------------------------------
>> >
>> -------------------------------------------------------------------------------
>> > ENTROPY RESULTS (QUASI-HARMONIC APPROXIMATION) CALCULATED WITH PTRAJ:
>> > Translational Rotational Vibrational
>> Total
>> > Complex: 16.7930 17.5417 888.2178
>> 922.5524
>> > Receptor: 16.3264 16.4191 744.8073
>> 777.5525
>> > Ligand: 15.9981 15.9934 736.5319
>> 768.5234
>> >
>> > DELTA S: -15.5315 -14.8708 -593.1214
>> -623.5235
>> >
>> -------------------------------------------------------------------------------
>> >
>> -------------------------------------------------------------------------------
>> >
>> > GENERALIZED BORN:
>> >
>> > Complex:
>> > Energy Component Average Std. Dev. Std. Err.
>> of
>> > Mean
>> >
>> -------------------------------------------------------------------------------
>> > BOND 844.4563 33.9946
>> > 1.6997
>> > ANGLE 2293.4877 33.7218
>> > 1.6861
>> > DIHED 1198.4857 18.1241
>> > 0.9062
>> > VDWAALS -1734.8917 22.4482
>> > 1.1224
>> > EEL -17168.3020 109.5404
>> > 5.4770
>> > 1-4 VDW 838.9863 12.0959
>> > 0.6048
>> > 1-4 EEL 12041.8362 58.1348
>> > 2.9067
>> > EGB -3376.9606 86.3362
>> > 4.3168
>> > ESURF 102.4703 1.7543
>> > 0.0877
>> >
>> > G gas -1685.9416 106.9086
>> > 5.3454
>> > G solv -3274.4903 85.9813
>> > 4.2991
>> >
>> > TOTAL -4960.4319 48.0756
>> > 2.4038
>> >
>> >
>> > Receptor:
>> > Energy Component Average Std. Dev. Std. Err.
>> of
>> > Mean
>> >
>> -------------------------------------------------------------------------------
>> > BOND 416.0058 16.0560
>> > 0.8028
>> > ANGLE 1278.9046 25.4859
>> > 1.2743
>> > DIHED 688.8077 14.2048
>> > 0.7102
>> > VDWAALS -1105.7934 15.2715
>> > 0.7636
>> > EEL -10471.9733 71.2250
>> > 3.5612
>> > 1-4 VDW 502.2180 9.2879
>> > 0.4644
>> > 1-4 EEL 7057.2247 31.7299
>> > 1.5865
>> > EGB -1272.0252 58.3189
>> > 2.9159
>> > ESURF 54.6697 1.3079
>> > 0.0654
>> >
>> > G gas -1634.6059 73.0947
>> > 3.6547
>> > G solv -1217.3554 57.6275
>> > 2.8814
>> >
>> > TOTAL -2851.9613 35.9199
>> > 1.7960
>> >
>> >
>> > Ligand:
>> > Energy Component Average Std. Dev. Std. Err.
>> of
>> > Mean
>> >
>> -------------------------------------------------------------------------------
>> > BOND 428.4505 29.8335
>> > 1.4917
>> > ANGLE 1014.5831 23.9354
>> > 1.1968
>> > DIHED 509.6780 12.6930
>> > 0.6346
>> > VDWAALS -618.2028 14.6859
>> > 0.7343
>> > EEL -6213.0919 78.1662
>> > 3.9083
>> > 1-4 VDW 336.7683 8.0045
>> > 0.4002
>> > 1-4 EEL 4984.6115 49.8345
>> > 2.4917
>> > EGB -2593.5910 69.7658
>> > 3.4883
>> > ESURF 50.4901 1.3869
>> > 0.0693
>> >
>> > G gas 442.7966 73.9919
>> > 3.6996
>> > G solv -2543.1009 69.0004
>> > 3.4500
>> >
>> > TOTAL -2100.3043 31.4666
>> > 1.5733
>> >
>> >
>> > Differences (Complex - Receptor - Ligand):
>> > Energy Component Average Std. Dev. Std. Err.
>> of
>> > Mean
>> >
>> -------------------------------------------------------------------------------
>> > BOND -0.0000 0.0001
>> > 0.0000
>> > ANGLE -0.0000 0.0001
>> > 0.0000
>> > DIHED -0.0000 0.0001
>> > 0.0000
>> > VDWAALS -10.8955 8.5405
>> > 0.4270
>> > EEL -483.2368 81.8501
>> > 4.0925
>> > 1-4 VDW 0.0000 0.0001
>> > 0.0000
>> > 1-4 EEL -0.0000 0.0000
>> > 0.0000
>> > EGB 488.6556 77.8583
>> > 3.8929
>> > ESURF -2.6895 1.3187
>> > 0.0659
>> >
>> > DELTA G gas -494.1323 85.3064
>> > 4.2653
>> > DELTA G solv 485.9660 76.9182
>> > 3.8459
>> >
>> > DELTA TOTAL -8.1663 10.2147
>> > 0.5107
>> >
>> >
>> >
>> -------------------------------------------------------------------------------
>> >
>> -------------------------------------------------------------------------------
>> > Using Quasi-harmonic Entropy Approximation: DELTA G binding = 615.3572
>> >
>> -------------------------------------------------------------------------------
>> >
>> -------------------------------------------------------------------------------
>> >
>> > --
>> >
>> > Regards,
>> >
>> > Dr. Vaibhav A. Dixit,
>> >
>> > Visiting Scientist at the Manchester Institute of Biotechnology (MIB),
>> The
>> > University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
>> > AND
>> > Assistant Professor,
>> > Department of Pharmacy,
>> > ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
>> > Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
>> > VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
>> > India.
>> > Phone No. +91 1596 255652, Mob. No. +91-7709129400,
>> > Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bits-2Dpilani.ac.in_pilani_vaibhavdixit_profile&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=2kJ1aOKnSibTqiK-TWXPNSVvqDfauz0F1mWoQIa4_LI&s=RHaCNG-Cv3Q83xScqEHXYdptD-OTIXXDENJz8Bz5kl8&e=
>> >
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_vaibhav-2Ddixit-2Db1a07a39_&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=2kJ1aOKnSibTqiK-TWXPNSVvqDfauz0F1mWoQIa4_LI&s=a-u4wgtU93sZ_0hJ9QnqogbFZyQN0vcnse4-SduFIM0&e=
>> >
>> > ORCID ID:
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__orcid.org_0000-2D0003-2D4015-2D2941&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=2kJ1aOKnSibTqiK-TWXPNSVvqDfauz0F1mWoQIa4_LI&s=ZQUTKw3RmQCStMMtGDM3Ij8GvmeUROfmBJQqpt1J9Q0&e=
>> >
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__scholar.google.co.in_citations-3Fuser-3DX876BKcAAAAJ-26hl-3Den-26oi-3Dsra&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=2kJ1aOKnSibTqiK-TWXPNSVvqDfauz0F1mWoQIa4_LI&s=RYUIDBebRXVtiksSVXMdLiJP8Ajjfvx6ztUBzlMzOhc&e=
>> >
>> > P Please consider the environment before printing this e-mail
>> > _______________________________________________
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>> > AMBER.ambermd.org
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=2kJ1aOKnSibTqiK-TWXPNSVvqDfauz0F1mWoQIa4_LI&s=jB-_Rv6UuS8T6SN5vQVIFNtzWHytmYNPjS_GCMxSEig&e=
>>
>> --
>> Dr. Adrian E. Roitberg
>> V.T. and Louise Jackson Professor in Chemistry
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
>
> Regards,
>
> Dr. Vaibhav A. Dixit,
>
> Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
> University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
> AND
> Assistant Professor,
> Department of Pharmacy,
> ▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
> Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
> VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
> India.
> Phone No. +91 1596 255652, Mob. No. +91-7709129400,
> Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
> http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
> https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
>
> ORCID ID: https://orcid.org/0000-0003-4015-2941
>
> http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
>
> P Please consider the environment before printing this e-mail
>
>
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
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Received on Mon Apr 19 2021 - 10:30:03 PDT
