AMBER: pb_bomb in setgrd()

From: <steven.j.enoch.gsk.com>
Date: Tue, 10 Aug 2004 11:34:42 +0100

I am trying to perform mm_pbsa calculations on a protein which has
approximately 16000 atoms (including ligand and a cap of water around the
actives site). When I run the mm_pbsa script I get an error 'PB Bomb in
pb_setgrd()'. It crashes for the calculation of the complex. Here is my
output file:


          -------------------------------------------------------
          Amber 8 SANDER Scripps/UCSF 2004
          -------------------------------------------------------

| Run on 08/10/2004 at 10:02:33
  [-O]verwriting output

File Assignments:
| MDIN: pbsa.in
| MDOUT: pbsa_com.1.out
|INPCRD: ./1h06__com.crd.1
| PARM: ../../../comp.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, epsout = 80.0,
  istrng = 0, radiopt = 0,
  sprob = 1.6, space = 0.5,
  maxitn = 1000,
  npbverb= 1,
  fillratio = 4,
  cutres=12,
 &end

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 08/10/04 Time = 10:00:46
 NATOM = 15807 NTYPES = 16 NBONH = 7940 MBONA = 8082
 NTHETH = 18201 MTHETA = 10984 NPHIH = 33944 MPHIA = 20594
 NHPARM = 0 NPARM = 0 NNB = 88185 NRES = 955
 NBONA = 8082 NTHETA = 10984 NPHIA = 20594 NUMBND = 59
 NUMANG = 124 NPTRA = 45 NATYP = 42 NPHB = 0
 IFBOX = 0 NMXRS = 49 IFCAP = 0 NEXTRA = 0
 NCOPY = 0


| Memory Use Allocated
| Real 585545
| Hollerith 95799
| Integer 794321
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 8051 kbytes
| 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 = 10, nsnb =
99999
     ipol = 0, gbsa = 0, iesp = 0
     dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
     surften = 0.00500
     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
 
 ======== PB Initialization ========
 
     Max PBMD Nonbonded Pairs: 9390834 3841101
 
  no. of atoms processed in PB initialization: 15807
    1 PRO N -0.202000 1.550000 1.612500
    2 PRO H2 0.312000 1.300000 1.067270
    3 PRO H3 0.312000 1.300000 1.067270
    4 PRO CD -0.012000 1.700000 1.649917

with the bottom half looking like:

15803 h06 H20 0.138610 1.300000 1.449911
15804 h06 C20 -0.120270 1.700000 1.649917
15805 h06 H21 0.140950 1.300000 1.449911
15806 h06 C21 -0.106130 1.700000 1.649917
15807 h06 H22 0.144970 1.300000 1.449911
  total system charge for PB 5.9999796242510612
  SAS Surface: setting up working radii
  SAS Surface: found nonzero radii 15807
  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 8473440
  NB-update: atom-based nb list 1795195
 
 
 ======== Setting up Grid Parameters ========
 Using bounding box for grid setup
 Bounding Box Center: 23.226 18.690 5.256
 Xmin, Xmax, Xmax-Xmin: -18.449 64.900 83.349
 Ymin, Ymax, Ymax-Ymin: -27.536 64.916 92.452
 Zmin, Zmax, Zmax-Zmin: -47.050 57.561 104.611
   beginning box center at level 1 23.226 18.690 5.256
   beginning box center at level 2 23.226 18.690 5.256
 Grid dimension at level 1 85 93 107
 Grid origin corrected at level 1 -148.774 -169.310 -210.744
 Grid dimension at level 2 183 201 225
 Grid origin corrected at level 2 -22.774 -31.810 -51.245
 PB bomb in pb_setgrd(): Allocation aborted 9*0, 2*4205, 0, 4205, 3*0,
 10*4205, 4*0

Does anybody know what is wrong? and how to fix it?

Many thanks in advance

Dr Steve Enoch
GlaxoSmithKline
Stevenage
UK

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Received on Tue Aug 10 2004 - 11:53:00 PDT
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