AMBER Archive (2004)

Subject: Re: AMBER: pb_bomb in setgrd()

From: Ray Luo (rluo_at_uci.edu)
Date: Tue Aug 10 2004 - 11:29:13 CDT

Steven,

Your FDPB grid dimension is 183 x201 x225. Make sure you have enough
memory on your server. The error message means that the memory
allocation failed. You can reduce the memory usage either by using a
large grid spacing (space=0.5 in your output file), or by using single
precision in pbsa and recompile.

To recompile pbsa in single precision, you can comment out the following
line in "pb_def.h", i.e.

change

#define PBDPREC

to

!#define PBDPREC

and "make clean" and "make install" again.

Best,
Ray

steven.j.enoch_at_gsk.com wrote:

>
> 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 

-- 
====================================================
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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