AMBER Archive (2004)

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

From: Ray Luo (rluo_at_uci.edu)
Date: Mon Jul 19 2004 - 07:22:26 CDT

Hi Steven,

The error message shows that the estimation of maximum pairs for
residue-based cutoff is too small. A larger cutoff, for example by
setting cutres=12 (default 10) usually works fine.

The current estimation, which is for explicit water simulations, tends
to give a number too small for implicit water simulations. This will be
revised in the next release.

All the best,
Ray

steven.j.enoch_at_gsk.com wrote:

>
> 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 

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

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