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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Received on Wed Jul 28 2004 - 09:53:00 PDT
