Custom Search
----
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.rosswalker.co.uk>
To: <amber.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.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.scripps.edu
> > [mailto:owner-amber.scripps.edu] On Behalf Of William Wei
> > Sent: Friday, August 18, 2006 08:12
> > To: amber.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.rosswalker.co.uk>
> > To: <amber.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.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.scripps.edu
> > > > [mailto:owner-amber.scripps.edu] On Behalf Of William Lianhu Wei
> > > > Sent: Thursday, August 17, 2006 19:31
> > > > To: amber.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.utoronto.ca
> > > > University of Toronto weilianhu.hotmail.com
> > > > 19 Russell St.
> > > > Toronto, Ontario
> > > > M5S 2S2,Canada
> > > > --------------------------------------------------------------
> > > > ---------
> > > > The AMBER Mail Reflector
> > > > To post, send mail to amber.scripps.edu
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> > > >
> > >
> > >
> > >
> > --------------------------------------------------------------
> > ---------
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> > >
> >
> > --------------------------------------------------------------
> > ---------
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> >
>
>
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Received on Wed Aug 23 2006 - 06:07:11 PDT