AMBER Archive (2004)

Subject: AMBER: PB bomb in pb_saarc

From: steven.j.enoch_at_gsk.com
Date: Wed Jul 28 2004 - 03:26:38 CDT

Amber users,

I am trying to perform mm-pbsa calculations on a protien-ligand complex of
6000 atoms, I can run a mm-gbsa calculation using the same trajectory file
without any problems, but when I try and run the pbsa calculation I get an
error message 'PB bomb in pb_saarc'. Does anybody know how to fix it?

Here is the input:

| Run on 07/28/2004 at 08:54:55
  [-O]verwriting output

File Assignments:
| MDIN: pbsa.in
| MDOUT: pbsa_com.1.out
|INPCRD: ./om1__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 = 07/28/04 Time = 08:30:29
 NATOM = 6000 NTYPES = 14 NBONH = 2959 MBONA = 3113
 NTHETH = 6704 MTHETA = 4230 NPHIH = 12712 MPHIA = 7800
 NHPARM = 0 NPARM = 0 NNB = 33076 NRES = 380
 NBONA = 3113 NTHETA = 4230 NPHIA = 7800 NUMBND = 56
 NUMANG = 120 NPTRA = 41 NATYP = 40 NPHB = 0
 IFBOX = 0 NMXRS = 124 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 222257
| Hollerith 36382
| Integer 311696
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 3096 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: 3564560 1458000
 
  no. of atoms processed in PB initialization: 6000
    1 GLU N 0.001700 1.550000 1.612500
    2 GLU H1 0.239100 1.300000 1.067270
    3 GLU H2 0.239100 1.300000 1.067270
    4 GLU H3 0.239100 1.300000 1.067270
    5 GLU CA 0.058800 1.700000 1.649917

with the bottom of the output and error message producing:

5999 om1 C28 -0.142080 1.700000 1.649917
 6000 om1 H5 0.109870 1.300000 1.449911
  total system charge for PB -13.999940249913722
  SAS Surface: setting up working radii
  SAS Surface: found nonzero radii 6000
  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 3356442
  NB-update: atom-based nb list 695086
 
 
 ======== Setting up Grid Parameters ========
 Using bounding box for grid setup
 Bounding Box Center: 15.813 3.146 8.627
 Xmin, Xmax, Xmax-Xmin: -14.383 46.009 60.392
 Ymin, Ymax, Ymax-Ymin: -28.572 34.863 63.435
 Zmin, Zmax, Zmax-Zmin: -20.030 37.284 57.314
   beginning box center at level 1 15.813 3.146 8.627
   beginning box center at level 2 15.813 3.146 8.627
 Grid dimension at level 1 61 65 59
 Grid origin corrected at level 1 -108.187 -128.855 -111.373
 Grid dimension at level 2 137 143 131
 Grid origin corrected at level 2 -18.687 -32.855 -24.373
 Number of SA srf points exposed 49096
 PB bomb in pb_saarc(): Allocation aborted 2*0, 4205

Many thanks for any help

Dr Steve Enoch
GlaxoSmithKline
UK

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