AMBER Archive (2006)

Subject: AMBER: Ask for help in pbsa error in AMBER9

From: Cheng Luo, Ph.D. (cluo_at_wistar.org)
Date: Thu Jun 08 2006 - 11:08:10 CDT

Dear Amber Member,

I met error when I use mmpbsa to calculate PB. The receptor and complex results are ok in the calculation. However, some error appeared in the step of calculation the lig. Here is the error result(in pbsa_lig.1.out file), the red part is the final report:

 
          -------------------------------------------------------
          Amber 9 PBSA Scripps/UCSF 2006
          -------------------------------------------------------
 
| Run on 06/07/2006 at 22:37:44
  [-O]verwriting output
 
File Assignments:
| MDIN: pbsa.in
| MDOUT: pbsa_lig.1.out
|INPCRD: ../snapshot/HST2_lig.crd.1
| PARM: ../lig.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 PB
 &cntrl
  ntf = 1, ntb = 0,
  igb = 10, dielc = 1.0,
  cut = 999.0, nsnb = 99999,
  scnb = 2.0, scee = 1.2,
  imin = 1, maxcyc = 0, ntmin = 2,
 &end
 &pb
  epsin = 1.0, epsout = 80.0,
  istrng = 0, radiopt = 0,
  sprob = 1.4, space = 0.5,
  maxitn = 1000, npopt = 1,
  cavity_surften = 0.0072, cavity_offset = 0.00,
  npbverb= 1
 &end
 
--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------
 
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/18/06 Time = 15:35:11
 NATOM = 15 NTYPES = 6 NBONH = 0 MBONA = 15
 NTHETH = 0 MTHETA = 22 NPHIH = 0 MPHIA = 37
 NHPARM = 0 NPARM = 0 NNB = 64 NRES = 1
 NBONA = 15 NTHETA = 22 NPHIA = 37 NUMBND = 8
 NUMANG = 12 NPTRA = 6 NATYP = 8 NPHB = 0
 IFBOX = 0 NMXRS = 15 IFCAP = 0 NEXTRA = 0
 NCOPY = 0
 
 
| Memory Use Allocated
| Real 596
| Hollerith 93
| Integer 20638
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 85 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
   2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
 
MOL
 
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 = 10, nsnb = 99999
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
     scnb = 2.00000, scee = 1.20000
 
Frozen or restrained atoms:
     ibelly = 0, ntr = 0
 
Energy minimization:
     maxcyc = 0, ncyc = 10, ntmin = 2
     dx0 = 0.01000, drms = 0.00010
 
 ======== Implicit Solvent Initialization ========
 
     Max Nonbonded Pairs: 113 113 113
 
  no. of atoms processed in PB initialization: 15
     Max Nonbonded Pairs: 113 113 113
 
  no. of atoms processed in PB initialization: 15
  NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
    1 MOL N1 nb -0.694600 -0.694600 0.294970 1.550000 1.550000
    2 MOL C1 ca 0.510340 0.510340 -0.653260 1.700000 1.700000
    3 MOL H1 h4 0.026060 0.026060 0.536400 1.300000 1.300000
    4 MOL C2 ca -0.495060 -0.495060 1.119320 1.700000 1.700000
    5 MOL C6 c 0.852580 0.852580 -1.203860 1.700000 1.700000
    6 MOL O1 o -0.591640 -0.591640 0.260940 1.500000 1.500000
    7 MOL N2 n -0.969740 -0.969740 0.691560 1.550000 1.550000
    8 MOL H5 hn 0.404360 0.404360 -0.565380 1.300000 1.300000
    9 MOL H6 hn 0.404360 0.404360 -0.565380 1.300000 1.300000
   10 MOL C3 ca 0.251460 0.251460 -0.656720 1.700000 1.700000
   11 MOL H2 ha 0.095990 0.095990 0.347450 1.300000 1.300000
   12 MOL C4 ca -0.509110 -0.509110 0.414660 1.700000 1.700000
   13 MOL H3 ha 0.193080 0.193080 -0.316030 1.300000 1.300000
   14 MOL C5 ca 0.479230 0.479230 -0.681780 1.700000 1.700000
   15 MOL H4 h4 0.042700 0.042700 0.521930 1.300000 1.300000
 
 total system charges (+/-) for PB 0.0000 3.2602 -3.2602
 cavity_surften = 0.0072 cavity_offset = 0.0000
 
  SAS Surface: surface dots generated: 366
 
--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
 
 
 begin time read from input coords = 0.000 ps
 
 Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------
 
  NB-update: residue-based nb list 43
  NB-update: atom-based nb list 105
 
 
 ======== Setting up Grid Parameters ========
 Using bounding box for grid setup
 Bounding Box Center: 37.000 36.000 47.500
 Xmin, Xmax, Xmax-Xmin: 33.288 40.869 7.581
 Ymin, Ymax, Ymax-Ymin: 33.071 38.704 5.633
 Zmin, Zmax, Zmax-Zmin: 42.977 51.922 8.945
   beginning box center at level 1 37.000 36.000 47.500
   beginning box center at level 2 37.000 36.000 47.500
 Grid dimension at level 1 5 5 5
 Grid origin corrected at level 1 25.000 24.000 35.500
 Grid dimension at level 2 29 25 33
 Grid origin corrected at level 2 29.500 29.500 39.000
PB Bomb in setgrd(): focusing grid too large 2
reset fillratio to a larger number 2.000

I changed the start snapshot and got same result. By the way, the nmode calculation in same snapshot is ok. So,anyone who can give me some advices is highly appreciated!

Thank you in advance!

Best regards,

Cheng Luo, Ph.D.

 
         
Cheng Luo, Ph.D.
Marmorstein's Lab
Room 327,3601 Spruce Street
The Wistar Institute
PA(19104) USA
Tel:215-898-2304
2006-06-08

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