AMBER Archive (2006)

Subject: Re: AMBER: GBSA EGB = NaN

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon Aug 21 2006 - 11:14:54 CDT

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/			-
  ---------------------------------------------------------------

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