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-- > > ---- > > 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 > > > > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > > > > > > > > > > > > > > > > > > > > > > > > -------------------------------------------------------------- > > > > --------- > > > > > The AMBER Mail Reflector > > > > > To post, send mail to amber.scripps.edu > > > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > > > > > > > > > > > > -------------------------------------------------------------- > > > > --------- > > > > The AMBER Mail Reflector > > > > To post, send mail to amber.scripps.edu > > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > > > > > > > > > > > > ----------------------------------------------------------------------- > > > The AMBER Mail Reflector > > > To post, send mail to amber.scripps.edu > > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > > > > > > ----------------------------------------------------------------------- > > The AMBER Mail Reflector > > To post, send mail to amber.scripps.edu > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > > > > > > -- > 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.scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu > ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo.scripps.eduReceived on Wed Aug 23 2006 - 06:07:11 PDT