AMBER Archive (2004)

Subject: AMBER: PB Bomb in pb_reslist(): maxnbr too small

From: steven.j.enoch_at_gsk.com
Date: Tue Jul 20 2004 - 08:00:59 CDT

Amber users,

I am trying to perform mm-pbsa calculations on a fairly large system, 5466
atoms. When I run the pbsa script I get the following error regarding a
PB Bomb in the pb_reslist. Does anybody know how to fix it?

Here is the top of my input

| Run on 07/20/2004 at 13:51:21
  [-O]verwriting output

File Assignments:
| MDIN: pbsa.in
| MDOUT: pbsa_com.1.out
|INPCRD: ./bs1__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,
 &end

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

| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 07/20/04 Time = 13:50:42
 NATOM = 5466 NTYPES = 15 NBONH = 2708 MBONA = 2812
 NTHETH = 6116 MTHETA = 3806 NPHIH = 11430 MPHIA = 6893
 NHPARM = 0 NPARM = 0 NNB = 29932 NRES = 344
 NBONA = 2812 NTHETA = 3806 NPHIA = 6893 NUMBND = 56
 NUMANG = 119 NPTRA = 44 NATYP = 40 NPHB = 0
 IFBOX = 0 NMXRS = 88 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

| Memory Use Allocated
| Real 202445
| Hollerith 33142
| Integer 283358
| Max Pairs 1
| Max Rstack 1
| Max Istack 1
| Total 2817 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: 2515827 1328238
 
  no. of atoms processed in PB initialization: 5466
    1 ARG N 0.130500 1.550000 1.612500
    2 ARG H1 0.208300 1.300000 1.067270
    3 ARG H2 0.208300 1.300000 1.067270
    4 ARG H3 0.208300 1.300000 1.067270

And here is the error message:

 5465 bs1 C80 -0.118820 1.700000 1.649917
 5466 bs1 H85 0.129990 1.300000 1.449911
  total system charge for PB -14.999970212980845
  SAS Surface: setting up working radii
  SAS Surface: found nonzero radii 5466
  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
--------------------------------------------------------------------------------

 PB bomb in pb_reslist(): maxnbr too small

Many thanks in advance for any help

Dr Steve Enoch
GlaxoSmithKline
UK

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