AMBER Archive (2006)

Subject: Re: AMBER: GBSA EGB = NaN

From: William Wei (william.wei_at_utoronto.ca)
Date: Mon Aug 21 2006 - 11:04:36 CDT

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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> > >
> > >
> > >
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