Dear Smith
Yeah you are right i loaded the ligand into VMD using Coordinates With
Periodic Box info. now i load without Periodic Box info and image looks
fine..But still calculation issue is there..
Regards
Sumra Wajid Abbasi
PhD Scholar
Computational Biology Lab, National Center for Bioinformatics
Quaid-e-Azam University, Islamabad-45320 Pakistan.
On Fri, Sep 20, 2013 at 6:05 AM, <wmsmith.uci.edu> wrote:
> Hello,
> Looking at the image of your ligand, there is definitely something odd.
> Are you using periodic boundaries when you load the ligand into VMD for
> viewing? When I loaded the ligand from the files you sent into VMD using
> Coordinates With Periodic Box info, it gives an image like you show.
> When I load without Periodic Box info, it shows up just fine.
>
> I will see if I can replicate the NaN error under PBSA itself to see if
> the source of the problem is there or something else.
> -Wes
>
> > 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
> >> _______________________________________________
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> >>
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Received on Thu Sep 19 2013 - 22:30:02 PDT
