Dear Jason
My input file consists of following parameters:
Input file for running PB and GB
&general
startframe=1, endframe=50, interval=1,
verbose=2, keep_files=0,
/
&gb
igb=5, saltcon=0.150,
/
&pb
istrng=0.15, fillratio=4.0
/
the command i used is:
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
amcligsolvated.prmtop -cp complex.prmtop -rp protein.prmtop -lp
ligand.prmtop -y amcprod1.mdcrd
command ran smooth no error appeared on terminal but when i checked output
file i came to know that NAN error in case of ligand occured because of
which no energy difference calculated.
Output was:
| Run on Tue Sep 17 17:20:17 2013
|
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB in serial
|&general
| endframe=50, keep_files=2,
|/
|&gb
| igb=2, saltcon=0.100,
|/
|&pb
| istrng=0.100,
|/
| --------------------------------------------------------------
|MMPBSA.py Version=12.0
|Solvated complex topology file: amcligsolvated.prmtop
|Complex topology file: amcliguUS.prmtop
|Receptor topology file: pro.prmtop
|Ligand topology file: unk.prmtop
|Initial mdcrd(s): amcprod1.mdcrd
|
|Receptor mask: ":1-357"
|Ligand mask: ":358"
|Ligand residue name is "UNK"
|
|Calculations performed using 50 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 1046.0599 25.0584
3.5438
ANGLE 2825.6096 27.8852
3.9436
DIHED 3867.0393 20.6518
2.9206
VDWAALS -2766.8957 18.9666
2.6823
EEL -22450.1018 52.8100
7.4685
1-4 VDW 1296.0772 16.0482
2.2696
1-4 EEL 14608.9084 34.7009
4.9074
EGB -4636.7135 33.1652
4.6903
ESURF 146.7058 1.1452
0.1620
G gas -1573.3031 55.6723
7.8733
G solv -4490.0077 33.3028
4.7097
TOTAL -6063.3108 43.9275
6.2123
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 1023.2391 25.1818
3.5612
ANGLE 2758.3780 27.3729
3.8711
DIHED 3808.4462 19.5218
2.7608
VDWAALS -2656.1969 18.4136
2.6041
EEL -22450.1018 52.8100
7.4685
1-4 VDW 1272.7137 15.8878
2.2469
1-4 EEL 14608.9084 34.7009
4.9074
EGB -4662.4389 33.1432
4.6872
ESURF 148.2532 1.1910
0.1684
G gas -1634.6133 55.0064
7.7791
G solv -4514.1857 33.2875
4.7076
TOTAL -6148.7990 44.1153
6.2389
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 22.8209 3.7323
0.5278
ANGLE 67.2316 5.6725
0.8022
DIHED 57.9771 3.3766
0.4775
VDWAALS -21.1078 1.7341
0.2452
1-4 VDW 23.3635 2.0523
0.2902
ESURF 8.4113 0.1439
0.0204
G gas 150.2853 7.8027
1.1035
G solv 8.4113 0.1439
0.0204
TOTAL 158.6965 7.8116
1.1047
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0000
0.0000
ANGLE -0.0000 0.0001
0.0000
DIHED 0.6160 0.3232
0.0457
VDWAALS -89.5910 3.1602
0.4469
EEL 0.0000 0.0000
0.0000
1-4 VDW -0.0000 0.0001
0.0000
1-4 EEL 0.0000 0.0000
0.0000
EGB 25.7254 1.2092
0.1710
ESURF -9.9586 0.2770
0.0392
DELTA G gas -88.9750 3.0895
0.4369
DELTA G solv 15.7667 1.1381
0.1610
DELTA TOTAL -73.2083 3.0542
0.4319
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 1046.0599 25.0584
3.5438
ANGLE 2825.6096 27.8852
3.9436
DIHED 3867.0393 20.6518
2.9206
VDWAALS -2766.8957 18.9666
2.6823
EEL -22450.1018 52.8100
7.4685
1-4 VDW 1296.0772 16.0482
2.2696
1-4 EEL 14608.9084 34.7009
4.9074
EPB -4507.0803 33.7185
4.7685
ENPOLAR 2907.4367 7.0087
0.9912
G gas -1573.3031 55.6723
7.8733
G solv -1599.6436 35.2985
4.9920
TOTAL -3172.9466 46.1397
6.5251
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 1023.2391 25.1818
3.5612
ANGLE 2758.3780 27.3729
3.8711
DIHED 3808.4462 19.5218
2.7608
VDWAALS -2656.1969 18.4136
2.6041
EEL -22450.1018 52.8100
7.4685
1-4 VDW 1272.7137 15.8878
2.2469
1-4 EEL 14608.9084 34.7009
4.9074
EPB -4549.0703 33.2881
4.7076
ENPOLAR 2865.0984 7.0316
0.9944
G gas -1634.6133 55.0064
7.7791
G solv -1683.9719 34.8674
4.9310
TOTAL -3318.5852 46.6278
6.5942
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 22.8209 3.7323
0.5278
ANGLE 67.2316 5.6725
0.8022
DIHED 57.9771 3.3766
0.4775
VDWAALS -21.1078 1.7341
0.2452
1-4 VDW 23.3635 2.0523
0.2902
EPB nan nan
nan
ENPOLAR 97.8510 0.8688
0.1229
G gas 150.2853 7.8027
1.1035
G solv nan nan
nan
TOTAL nan nan
nan
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0000
0.0000
ANGLE -0.0000 0.0001
0.0000
DIHED 0.6160 0.3232
0.0457
VDWAALS -89.5910 3.1602
0.4469
EEL 0.0000 0.0000
0.0000
1-4 VDW -0.0000 0.0001
0.0000
1-4 EEL 0.0000 0.0000
0.0000
EPB nan nan
nan
ENPOLAR -55.5128 1.3871
0.1962
EDISPER 0.0000 0.0000
0.0000
DELTA G gas -88.9750 3.0895
0.4369
DELTA G solv nan nan
nan
DELTA TOTAL nan nan
nan
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
when i visualized prmtop and MMBPSA.py generated mdcrds i found
a distorted ligand. i also tried MMPBSA.pl but no results.
kindly attached image of ligand hopefully these would be helpful for you
Regards
Sumra Wajid Abbasi
PhD Scholar
Computational Biology Lab, National Center for Bioinformatics
Quaid-e-Azam University, Islamabad-45320 Pakistan.
On Thu, Sep 19, 2013 at 3:41 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Sep 19, 2013 at 4:15 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
> sumra.msbi30.iiu.edu.pk> wrote:
>
> > Dear Jason
> >
> > NAN= No Atom Name
> >
>
> Actually NaN means "Not a Number." [http://en.wikipedia.org/wiki/NaN]
> It is an almost universal sign of some type of problem (either user or
> programmer).
>
> EPB/EGB = the electrostatic contribution to the solvation free energy
> > calculated by PB or GB respectively
> > ECAVITY = nonpolar contribution to the solvation free energy calculated
> by
> > an empirical model
> >
>
> You misunderstood me. I'm aware of what all of these terms mean. What is
> important when debugging is _which_ terms had NaN as their respective
> values? Since the solvation free energy is NaN, that means either the
> polar solvation term (EPB/EGB) or the non-polar solvation term (ECAVITY,
> ESURF, EDISPER) must be NaN (or both). Knowing this gives clues about
> where to look for problems. Of course you also omitted the G gas term from
> your email, so there could be problems there as well.
>
> I have visualized MMPBSA.py generated mdcrds using VMD...what i feel is
> > there are abnormalities in ligand geometry and also few in receptor..
> >
>
> This does not help, as it leaves me to "guess" what the 'abnormalities' are
> (and what you would consider 'normal'). For instance:
> http://www.mybiosoftware.com/wp-content/uploads/2011/03/AmberTools.jpg
> and http://archive.ambermd.org/201103/att-0730/Picture_2.png are two
> different 'abnormalities' which have quite different root causes and
> solutions. A picture is worth more than any number of words in this case.
>
> As general advice when asking questions of this nature, you will receive
> helpful answers far faster if you provide a good amount of details. Show
> the full output (not just lines you find troubling, because those are often
> not helpful by themselves). Show the exact commands that you used and any
> error messages or outputs that were produced. Also say how you tried to
> fix or debug it, and what you learned (or think you learned) in the
> process. Otherwise, the first few days will be spent trading emails of
> this sort...
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
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Received on Thu Sep 19 2013 - 07:00:03 PDT
