AMBER Archive (2006)

Subject: Re: AMBER: GBSA EGB = NaN

From: William Wei (william.wei_at_utoronto.ca)
Date: Mon Aug 21 2006 - 11:37:47 CDT

Dear Ilyas,

I tried cut=24. I had no luck on this issue. Thanks for your suggestion.

William

----- Original Message -----
From: "Ilyas Yildirim" <yildirim_at_pas.rochester.edu>
To: <amber_at_scripps.edu>
Sent: Monday, August 21, 2006 12:14 PM
Subject: Re: AMBER: GBSA EGB = NaN

> Dear William,
>
> In the ' 2. CONTROL DATA FOR THE RUN' section of your .out file,
> the cut is 'cut =**********'. That might cause the NaN problem. Maybe
> changing the cutoff value to something else will make things work. Good
> luck.
>
> Best,
>
> On Mon, 21 Aug 2006, William Wei wrote:
>
> > Dear Ross,
> >
> > I tried to run the mdin file generated by mm-pbsa, and did not find any
> > abnormal output. That give the same EGB=NaN. I generted the structure
from
> > my .crd and .top files, I checked using sybyl, I did not see any
improper
> > contact or bond. The VDWAALS and BOND items are okay. (I will attach
the
> > output from the seperate run).
> >
> > For the IGB, I used 4. The amberversion I am using is amber 7. Is this
> > version too old? I do not know if this version have option IGB=5 or
not.
> >
> > Thank you again for your help,
> > William
> >
> > ###Complex sander input file:
> > File generated by mm_pbsa.pl. Using MM GB
> > &cntrl
> > ntf = 1, ntb = 0, dielc = 1,
> > idecomp= 0,
> > igb = 4, saltcon= 0.00,
> > offset = 0, extdiel= 80.0,
> > gbsa = 0, surften= 1.0,
> > cut = 99999.0, nsnb = 99999,
> > scnb = 2.0, scee = 1.2,
> >
> > imin = 1, maxcyc = 1, ncyc = 0,
> > &end
> >
> > ### sander output file:
> >
> > -------------------------------------------------------
> > Amber 7 SANDER Scripps/UCSF 2002
> > -------------------------------------------------------
> >
> > | Mon Aug 21 11:41:16 2006
> >
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: ./sander_com.in
> > | MDOUT: ./sander_com_test.out
> > |INPCRD: ../sn_test_20/ODC_OMP_com.crd
> > | PARM: ../ODCase_Com.top
> > |RESTRT: restrt
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDEN: mden
> > | MDCRD: mdcrd
> > |MDINFO: mdinfo
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> >
> >
> > Here is the input file:
> >
> > File generated by mm_pbsa.pl. Using MM GB
> > &cntrl
> > ntf = 1, ntb = 0, dielc = 1,
> > idecomp= 0,
> > igb = 4, saltcon= 0.00,
> > offset = 0, extdiel= 80.0,
> > gbsa = 0, surften= 1.0,
> > cut = 99999.0, nsnb = 99999,
> > scnb = 2.0, scee = 1.2,
> >
> > imin = 1, maxcyc = 1, ncyc = 0,
> > &end
> >
>
> -------------------------------------------------------------------------- 

--
> > ----
> >    1.  RESOURCE   USE:
>
> --------------------------------------------------------------------------
--
> > ----
> >
> > | Flags: SGIFFT MEM_ALLOC MPI RLE ROWAT HAS_10_12 HAS_FTN_ERFC
> > | New format PARM file being parsed.
> > | Version =    1.000 Date = 08/01/06 Time = 15:42:24
> >  NATOM  =    6430 NTYPES =      18 NBONH =    3216 MBONA  =    3262
> >  NTHETH =    7318 MTHETA =    4412 NPHIH =   13512 MPHIA  =    8232
> >  NHPARM =       0 NPARM  =       0 NNB   =   35364 NRES   =     420
> >  NBONA  =    3262 NTHETA =    4412 NPHIA =    8232 NUMBND =      44
> >  NUMANG =      94 NPTRA  =      47 NATYP =      30 NPHB   =       0
> >  IFBOX  =       0 NMXRS  =      34 IFCAP =       0 NEXTRA =       0
> >
> >
> > |     Memory Use     Allocated
> > |     Real              257515
> > |     Hollerith          39002
> > |     Integer           384888
> > |     Max Pairs              1
> > |     Max Rstack         96450
> > |     Max Istack         32150
> > | Duplicated    0 dihedrals
> > | Duplicated    0 dihedrals
> >
>
> --------------------------------------------------------------------------
--
> > ----
> >    2.  CONTROL  DATA  FOR  THE  RUN
>
> --------------------------------------------------------------------------
--
> > ----
> >
> >
> >
> > General flags:
> >      imin    =       1, nmropt  =       0
> >
> > Nature and format of input:
> >      ntx     =       1, irest   =       0, ntrx    =       1
> >
> > Nature and format of output:
> >      ntxo    =       1, ntpr    =      50, ntrx    =       1, ntwr    =
> > 500
> >      iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =
> > 0
> >      ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=
> > 0
> >
> > Potential function:
> >      ntf     =       1, ntb     =       0, igb     =       4, nsnb    =
> > 99999
> >      ipol    =       0, gbsa    =       0
> >      dielc   =   1.00000, cut     =**********, intdiel =   1.00000
> >      saltcon =   0.00000, offset  =   0.00000, gbalpha=    1.00000
> >      gbbeta  =   0.00000, gbgamma =   0.00000, surften =   1.00000
> >      scnb    =   2.00000, scee    =   1.20000
> >
> > Frozen or restrained atoms:
> >      ibelly  =       0, ntr     =       0
> >
> > Energy minimization:
> >      maxcyc  =       1, ncyc    =       0, ntmin   =       1
> >      dx0     =   0.01000, dxm     =   0.50000, drms    =   0.00010
> > | PLEVEL = 1: runmd parallelization, no EKCMR
> >
>
> --------------------------------------------------------------------------
--
> > ----
> >    3.  ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------
--
> > ----
> >
> >
> >  begin time read from input coords =     0.000 ps
> >
> > | Reorder water Setup:
> > |   ----- Reordering water will NOT be done
> > |      Does not work with minimization
> > |
> >  Number of triangulated 3-point waters found:        0
> > |  Atom division among processors:
> > |         0    6430
> > |  Running AMBER/MPI version on    1 nodes
> >
> >
>
> --------------------------------------------------------------------------
--
> > ----
> >    4.  RESULTS
>
> --------------------------------------------------------------------------
--
> > ----
> >
> >
> >
> >    NSTEP       ENERGY          RMS            GMAX         NAME
NUMBER
> >       1              NaN            NaN     0.0000E+00     N           1
> >
> >  BOND    =     1198.5268  ANGLE   =     3183.2750  DIHED      =
> > 3858.7614
> >  VDWAALS =    -3497.1212  EEL     =   -31925.1169  EGB        =
> > NaN
> >  1-4 VDW =     1484.4497  1-4 EEL =    21392.8129  RESTRAINT  =
> > 0.0000
> >   MAXIMUM NUMBER OF F EVALUATION EXCEEDED
> >
> >
> >                     FINAL RESULTS
> >
> >
> >
> >    NSTEP       ENERGY          RMS            GMAX         NAME
NUMBER
> >       1              NaN            NaN     0.0000E+00     N           1
> >
> >  BOND    =     1198.5268  ANGLE   =     3183.2750  DIHED      =
> > 3858.7614
> >  VDWAALS =    -3497.1212  EEL     =   -31925.1169  EGB        =
> > NaN
> >  1-4 VDW =     1484.4497  1-4 EEL =    21392.8129  RESTRAINT  =
> > 0.0000
> >
>
> --------------------------------------------------------------------------
--
> > ----
> >    5.  TIMINGS
>
> --------------------------------------------------------------------------
--
> > ----
> >
> > |    Read coords time           0.04 ( 0.07% of Total)
> > |                Calc gb radii              9.40 (19.04% of Gen B)
> > |                Calc gb diag              18.47 (37.43% of Gen B)
> > |                Calc gb off-diag          21.47 (43.52% of Gen B)
> > |             Gen Born time             49.34 (100.0% of Nonbo)
> > |          Nonbond force             49.34 (99.86% of Force)
> > |          Angle energy               0.02 ( 0.05% of Force)
> > |          Dihedral energy            0.04 ( 0.09% of Force)
> > |       Force time                49.41 (100.0% of Runmd)
> > |    Runmd Time                49.41 (98.35% of Total)
> > |    Other                      0.79 ( 1.58% of Total)
> > | Total time                50.24 (100.0% of ALL  )
> >
> > | Highest rstack allocated:      96450
> > | Highest istack allocated:      12860
> >
> > |     Setup wallclock           1 seconds
> > |     Nonsetup wallclock       49 seconds
> > ##############
> >
> > ----- Original Message -----
> > From: "Ross Walker" <ross_at_rosswalker.co.uk>
> > To: <amber_at_scripps.edu>
> > Sent: Friday, August 18, 2006 6:11 PM
> > Subject: RE: AMBER: GBSA EGB = NaN
> >
> >
> > > Dear William,
> > >
> > > I was more interested in seeing the mdin file greated by mmpbsa. Can
you
> > run
> > > the calculation manually outside of the mm-pbsa script. What happens
in
> > this
> > > case?
> > >
> > > There is nothing that looks strange in your output files so it is
unlikely
> > > that you have a bad structure. Do the tests cases all pass? Have you
tried
> > > setting up a simple GB calculation of your system independently of
mmpbsa
> > > and verified that this give the same problem?
> > >
> > > I would also try recreating the prmtop file and then also taking a
look at
> > > the section labelled:
> > >
> > > %FLAG RADII
> > > %FORMAT(5E16.8)
> > >
> > > Does anything look weird here. Most of these numbers should be around
0.1
> > to
> > > 2.0. I would pay close attention to anything that is not.
> > >
> > > Also which version of GB are you using? I know there can be some
issues
> > with
> > > IGB=1 or 2 although I forget specifically what the issues are -
perhaps
> > > someone else on the list can contribute here. If you are using IGB=1
or 2
> > > try using IGB=5 and see if this fixes the problem.
> > >
> > > All the best
> > > Ross
> > >
> > > /\
> > > \/
> > > |\oss Walker
> > >
> > > | HPC Consultant and Staff Scientist |
> > > | San Diego Supercomputer Center |
> > > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > > | http://www.rosswalker.co.uk | PGP Key available on request |
> > >
> > > Note: Electronic Mail is not secure, has no guarantee of delivery, may
not
> > > be read every day, and should not be used for urgent or sensitive
issues.
> > >
> > > > -----Original Message-----
> > > > From: owner-amber_at_scripps.edu
> > > > [mailto:owner-amber_at_scripps.edu] On Behalf Of William Wei
> > > > Sent: Friday, August 18, 2006 08:12
> > > > To: amber_at_scripps.edu
> > > > Subject: Re: AMBER: GBSA EGB = NaN
> > > >
> > > > Dear Ross,
> > > >
> > > > At the beginning of my calculation, it was running sander with the
> > > > snapshots.  I did not see anything unusual.  My system is not
> > > > big, as about
> > > > 6430atoms in my complex.   I am using SGI Onyx 3800 with IRIX
> > > > 6.5 system.
> > > > Here is my input file and the output of my complex.
> > > >
> > > > Thank you very much,
> > > > William
> > > > GBSA input:
> > > > @GENERAL
> > > > #
> > > > PREFIX ODC_OMP
> > > > PATH ../sn_test_20/
> > > > #
> > > > COMPLEX 1
> > > > RECEPTOR 1
> > > > LIGAND 1
> > > >
> > > > #
> > > > #
> > > >
> > > > COMPT ../ODCase_Com.top
> > > >
> > > > RECPT ../ODCase_Rec.top
> > > >
> > > > LIGPT ../ODCase_Lig.top
> > > >
> > > > #
> > > >
> > > > GC 0
> > > >
> > > > AS 0
> > > >
> > > > DC 0
> > > >
> > > > #
> > > >
> > > > MM 1
> > > >
> > > > GB 1
> > > >
> > > > PB 0
> > > >
> > > > MS 1
> > > >
> > > > #
> > > >
> > > > NM 0
> > > >
> > > > #
> > > >
> > > > ##############################################################
> > > > ##############
> > > > ####
> > > >
> > > > @DELPHI
> > > >
> > > > #
> > > >
> > > > #
> > > >
> > > > FOCUS 0
> > > >
> > > > INDI 1.0
> > > >
> > > > EXDI 80.0
> > > >
> > > > PERFIL 80.0
> > > >
> > > > SCALE 2
> > > >
> > > > LINIT 1000
> > > >
> > > > BNDCON 4
> > > >
> > > > #CHARGE ../my_amber94_delphi.crg
> > > >
> > > > #SIZE ../my_parse_delphi.siz
> > > >
> > > > CHARGE ../amber94_delphi_OMP.crg
> > > >
> > > > SIZE ../parseres_OMP.siz
> > > >
> > > > #
> > > >
> > > > SURFTEN 0.00542
> > > >
> > > > SURFOFF 0.92
> > > >
> > > > #
> > > >
> > > > ##############################################################
> > > > ##############
> > > > ####
> > > >
> > > > @GB
> > > >
> > > > #
> > > >
> > > > # GB parameters
> > > >
> > > > #
> > > >
> > > > IGB 4
> > > >
> > > > SALTCON 0.00
> > > >
> > > > EXTDIEL 80.0
> > > >
> > > > #
> > > >
> > > > SURFTEN 0.0072
> > > >
> > > > SURFOFF 0.00
> > > >
> > > > #
> > > > ##############################################################
> > > > ##############
> > > > ####
> > > >
> > > > @MS
> > > > #
> > > > # Molsurf parameters
> > > > #
> > > > # PROBE - Radius of the probe sphere used to calculate the SAS.
> > > >
> > > > # RADII - Name of the radii file.
> > > > #
> > > > PROBE 1.4
> > > >
> > > > #RADII ../atmtypenumbers
> > > >
> > > > RADII ../atmtypenumbers_OMP
> > > > #
> > > > ##############################################################
> > > > ##############
> > > > #####
> > > >
> > > > @PROGRAMS
> > > > #
> > > > # Program executables and paths
> > > > #
> > > > #DELPHI /home/gohlke/src/delphi.98/exe.R10000/delphi
> > > > DELPHI /aspirin/william/Software/delphi/IRIX/delphi
> > > > #
> > > > ##############################################################
> > > > ##############
> > > > ####
> > > >
> > > >
> > > >
> > > > Output of my complex:
> > > > MM
> > > > GB
> > > > MS
> > > > 1
> > > >  BOND    =     1198.5268  ANGLE   =     3183.2750  DIHED      =
> > > > 3858.7614
> > > >  VDWAALS =    -3497.1212  EEL     =   -31925.1169  EGB        =
> > > > NaN
> > > >  1-4 VDW =     1484.4497  1-4 EEL =    21392.8129  RESTRAINT  =
> > > > 0.0000
> > > > surface area =  15877.709
> > > > 2
> > > >  BOND    =     1249.4284  ANGLE   =     3112.2372  DIHED      =
> > > > 3852.2178
> > > >  VDWAALS =    -3529.7154  EEL     =   -31904.5266  EGB        =
> > > > NaN
> > > >  1-4 VDW =     1476.8527  1-4 EEL =    21318.8379  RESTRAINT  =
> > > > 0.0000
> > > > surface area =  15876.309
> > > > 3
> > > >  BOND    =     1206.7192  ANGLE   =     3145.3704  DIHED      =
> > > > 3880.0414
> > > >  VDWAALS =    -3512.8353  EEL     =   -31834.1365  EGB        =
> > > > NaN
> > > >  1-4 VDW =     1508.3817  1-4 EEL =    21321.6349  RESTRAINT  =
> > > > 0.0000
> > > > surface area =  15878.668
> > > > 4
> > > >  BOND    =     1236.1746  ANGLE   =     3158.5354  DIHED      =
> > > > 3869.2900
> > > >  VDWAALS =    -3485.6651  EEL     =   -31855.4143  EGB        =
> > > > NaN
> > > >  1-4 VDW =     1461.7513  1-4 EEL =    21376.0072  RESTRAINT  =
> > > > 0.0000
> > > > surface area =  15798.397
> > > > 5
> > > >  BOND    =     1247.7303  ANGLE   =     3273.7533  DIHED      =
> > > > 3876.9796
> > > >  VDWAALS =    -3534.9529  EEL     =   -31871.1197  EGB        =
> > > > NaN
> > > >  1-4 VDW =     1458.7460  1-4 EEL =    21307.7514  RESTRAINT  =
> > > > 0.0000
> > > > surface area =  15895.754
> > > > 6
> > > >  BOND    =     1241.4778  ANGLE   =     3222.0305  DIHED      =
> > > > 3925.6273
> > > >  VDWAALS =    -3488.7917  EEL     =   -31868.4341  EGB        =
> > > > NaN
> > > >  1-4 VDW =     1480.5582  1-4 EEL =    21310.2085  RESTRAINT  =
> > > > 0.0000
> > > > surface area =  15913.447
> > > > 7
> > > >  BOND    =     1246.3852  ANGLE   =     3210.2564  DIHED      =
> > > > 3940.9817
> > > >  VDWAALS =    -3559.4844  EEL     =   -31873.9004  EGB        =
> > > > NaN
> > > >  1-4 VDW =     1471.1604  1-4 EEL =    21342.0148  RESTRAINT  =
> > > > 0.0000
> > > > surface area =  15736.376
> > > > 8
> > > >  BOND    =     1239.2338  ANGLE   =     3248.2204  DIHED      =
> > > > 3892.2518
> > > >  VDWAALS =    -3497.6510  EEL     =   -31832.1607  EGB        =
> > > > NaN
> > > >  1-4 VDW =     1449.2936  1-4 EEL =    21270.9055  RESTRAINT  =
> > > > 0.0000
> > > > surface area =  15745.638
> > > >
> > > >
> > > > ----- Original Message -----
> > > > From: "Ross Walker" <ross_at_rosswalker.co.uk>
> > > > To: <amber_at_scripps.edu>
> > > > Sent: Thursday, August 17, 2006 10:57 PM
> > > > Subject: RE: AMBER: GBSA EGB = NaN
> > > >
> > > >
> > > > > Dear William,
> > > > >
> > > > > Can you post the input files you used both for
> > > > equilibration and the GB
> > > > part
> > > > > of the run. Also include the first few steps of the output
> > > > file so we can
> > > > > look more carefully. What happens if you run the
> > > > calculation from the
> > > > > beginning with GB turned on? E.g. during the initial
> > > > minimisation - do you
> > > > > get a problem here? Also do all the GB test cases work? And
> > > > how big is
> > > > your
> > > > > molecule? What is you hardware (compilers, math library
> > > > etc). I have come
> > > > > across bugs in IBM's MASSV library on Blue Gene systems
> > > > where you would
> > > > get
> > > > > NaN for GB simulations on more than about 20,000 atoms
> > > > (vexp on vector
> > > > > lengths of > 10^8 gives NaN's) but this is a very specific
> > > > case. There
> > > > could
> > > > > be other systems that have bugs in their vector math
> > > > libraries though. But
> > > > > first of all before we jump to conclusions it would be good
> > > > to see all
> > > > your
> > > > > input and output files.
> > > > >
> > > > > All the best
> > > > > Ross
> > > > >
> > > > > /\
> > > > > \/
> > > > > |\oss Walker
> > > > >
> > > > > | HPC Consultant and Staff Scientist |
> > > > > | San Diego Supercomputer Center |
> > > > > | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> > > > > | http://www.rosswalker.co.uk | PGP Key available on request |
> > > > >
> > > > > Note: Electronic Mail is not secure, has no guarantee of
> > > > delivery, may not
> > > > > be read every day, and should not be used for urgent or
> > > > sensitive issues.
> > > > >
> > > > > > -----Original Message-----
> > > > > > From: owner-amber_at_scripps.edu
> > > > > > [mailto:owner-amber_at_scripps.edu] On Behalf Of William Lianhu Wei
> > > > > > Sent: Thursday, August 17, 2006 19:31
> > > > > > To: amber_at_scripps.edu
> > > > > > Subject: AMBER: GBSA EGB = NaN
> > > > > >
> > > > > > Dear all,
> > > > > >
> > > > > > I finished molecular dynamics simulation of my system about
> > > > > > 3ns.  From the
> > > > > > energy profile, the system reached equilibrium at about 1.5
> > > > > > ns.  I was trying
> > > > > > to calculate the binding free energy.  The trajectories I
> > > > > > used was after
> > > > > > 1.5ns.  No matter which trajectory I used, I always got
> > > > > > EGB=NaN (on Complex
> > > > > > and receptor), and the program stopped at statistical
> > > > > > calculation.  The VDW
> > > > > > contribution is okay. Does anyone meet this before, or give
> > > > > > me any clue for
> > > > > > that.  In 2004 archive, there is somebody asked this, but
> > > > > > there was no reply
> > > > > > for this.  Thanks in advance.
> > > > > >
> > > > > > William
> > > > > >
> > > > > > --
> > > > > > --------------------------------------------------------------
> > > > > > William Wei                      Tel: +1-416-946-7551
> > > > > > Faculty of Pharmacy            Email: william.wei_at_utoronto.ca
> > > > > > University of Toronto                 weilianhu_at_hotmail.com
> > > > > > 19 Russell St.
> > > > > > Toronto, Ontario
> > > > > > M5S 2S2,Canada
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> --
>   Ilyas Yildirim
>   ---------------------------------------------------------------
>   - Department of Chemisty       - -
>   - University of Rochester      - -
>   - Hutchison Hall, # B10        - -
>   - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office) -
>   - http://www.pas.rochester.edu/~yildirim/ -
>   ---------------------------------------------------------------
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

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The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu