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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Received on Tue Jul 20 2004 - 14:53:00 PDT
