Dear Dr. Ray Luo,
Sorry for replying so late...actualyy i checked the output file, found an erro..rectified it and re-ran the command:
mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
i got the follwing error:
/opt/amber10/exe/sander -O -i pbsa_com.in -o pb sa_com.7.out -c /home/bharatam/amberresults_w/amberresults31/snapshot_com.crd.7 -p /home/bha ratam/amberresults_w/amb31/A31.prmtop not successful
the contents of the output file are pasted below:
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 06/05/2009 at 15:43:50
[-O]verwriting output
File Assignments:
| MDIN: pbsa_com.in
| MDOUT: pbsa_com.7.out
|INPCRD: /home/bharatam/amberresults_w/amberresults31/snapshot_com.crd.7
| PARM: /home/bharatam/amberresults_w/amb31/A31.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
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,
ivcap = 0, cutcap = -1,
xcap = 0, ycap = 0, zcap = 0
idecomp= 0,
&end
&pb
epsin = 1.0, epsout = 80.0,
istrng = 0.0, radiopt = 0,
sprob = 1.4, space = 0.5,
maxitn = 1000, npopt = 1, dbfopt = 1,
cavity_surften = 0.0072, cavity_offset = 0.00,
pbtemp = 300.0,
fillratio = 4.0 npbverb= 1
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 05/25/09 Time = 15:24:22
NATOM = 3777 NTYPES = 14 NBONH = 1904 MBONA = 1908
NTHETH = 4330 MTHETA = 2563 NPHIH = 8175 MPHIA = 5873
NHPARM = 0 NPARM = 0 NNB = 20879 NRES = 224
NBONA = 1908 NTHETA = 2563 NPHIA = 5873 NUMBND = 52
NUMANG = 108 NPTRA = 51 NATYP = 39 NPHB = 0
IFBOX = 0 NMXRS = 44 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are modified Bondi radii (mbondi)
| Memory Use Allocated
| Real 242174
| Hollerith 22888
| Integer 213271
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 2814 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
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
======== Implicit Solvent Initialization ========
Max Nonbonded Pairs: 4249125 917811 7132865
no. of atoms processed in PB initialization: 3777
NUM RESI NAME TYPE CHARGE ATM CRG/H GRP CRG PB RADI NP RADI
1 MET N N3 0.159200 0.754400 0.888100 1.550000 1.550000
2 MET H1 H 0.198400 0.000000 0.000000 1.300000 1.300000
....
...
....
....
....
....
....3741 M_4 C2 c3 0.167121 0.155371 -0.079574 1.700000 1.700000
3742 M_4 H2 hc -0.005875 -0.005875 -0.005875 1.300000 1.300000
3743 M_4 H15 hc -0.005875 -0.005875 -0.005875 1.300000 1.300000
3744 M_4 C4 ca -0.078846 -0.078846 0.144835 1.700000 1.700000
3745 M_4 C9 ca -0.107028 0.034155 -0.192893 1.700000 1.700000
3746 M_4 C8 ca -0.321534 -0.148202 0.293820 1.700000 1.700000
3747 M_4 H3 ha 0.173332 0.173332 0.173332 1.300000 1.300000
3748 M_4 H6 ha 0.141183 0.141183 0.141183 1.300000 1.300000
3749 M_4 C5 ca -0.107028 0.034155 -0.192893 1.700000 1.700000
3750 M_4 H5 ha 0.141183 0.141183 0.141183 1.300000 1.300000
3751 M_4 C6 ca -0.321534 -0.148202 0.293820 1.700000 1.700000
3752 M_4 H4 ha 0.173332 0.173332 0.173332 1.300000 1.300000
3753 M_4 C7 ca 0.407867 0.407867 -0.274762 1.700000 1.700000
3754 M_4 O3 os -0.386225 -0.386225 0.268150 1.500000 1.500000
3755 M_4 C16 c3 0.216240 0.246508 -0.191950 1.700000 1.700000
3756 M_4 H19 h1 0.015134 0.015134 0.015134 1.300000 1.300000
3757 M_4 H20 h1 0.015134 0.015134 0.015134 1.300000 1.300000
3758 M_4 C15 c3 -0.202531 -0.052233 0.539870 1.700000 1.700000
3759 M_4 H14 hc 0.075149 0.075149 0.075149 1.300000 1.300000
3760 M_4 H18 hc 0.075149 0.075149 0.075149 1.300000 1.300000
3761 M_4 C14 c3 0.362373 0.345595 -0.134888 1.700000 1.700000
3762 M_4 H8 h1 -0.008389 -0.008389 -0.008389 1.300000 1.300000
3763 M_4 H9 h1 -0.008389 -0.008389 -0.008389 1.300000 1.300000
3764 M_4 O4 os -0.428250 -0.428250 -0.329184 1.500000 1.500000
3765 M_4 C11 ca -0.246529 -0.246529 0.593314 1.700000 1.700000
3766 M_4 C10 ca 0.315820 0.448944 -0.600706 1.700000 1.700000
3767 M_4 H7 h4 0.133124 0.133124 0.133124 1.300000 1.300000
3768 M_4 N1 nb -0.803121 -0.803121 0.693260 1.550000 1.550000
3769 M_4 C12 ca 1.047437 1.047437 -0.763398 1.700000 1.700000
3770 M_4 N3 nh -0.974766 -0.177972 0.869465 1.550000 1.550000
3771 M_4 H10 hn 0.398397 0.398397 0.398397 1.300000 1.300000
3772 M_4 H11 hn 0.398397 0.398397 0.398397 1.300000 1.300000
3773 M_4 N2 nb -0.829742 -0.829742 1.036844 1.550000 1.550000
3774 M_4 C13 ca 0.819149 0.819149 -0.390502 1.700000 1.700000
3775 M_4 N4 nh -0.956186 -0.133380 0.685769 1.550000 1.550000
3776 M_4 H12 hn 0.411403 0.411403 0.411403 1.300000 1.300000
3777 M_4 H13 hn 0.411403 0.411403 0.411403 1.300000 1.300000
total system charges (+/-) for PB 9.0000 420.3270 -411.3270
cavity_surften = 0.0072 cavity_offset = 0.0000
SAS Surface: surface dots generated: 366
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
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 1383768
NB-update: atom-based nb list 53172
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 47.000 43.500 29.000
Xmin, Xmax, Xmax-Xmin: -6.933 100.641 107.574
Ymin, Ymax, Ymax-Ymin: -18.558 105.341 123.899
Zmin, Zmax, Zmax-Zmin: -29.798 88.266 118.064
beginning box center at level 1 47.000 43.500 29.000
beginning box center at level 2 47.000 43.500 29.000
Grid dimension at level 1 109 125 119
Grid origin corrected at level 1 -173.000 -208.500 -211.000
Grid dimension at level 2 229 263 251
Grid origin corrected at level 2 -10.500 -22.500 -34.000
SA surface: setting up working radii
SA surface: found nonzero radii 3777
Number of SA srf points exposed455488
SA Bomb in sa_arc(): Allocation aborted 0 0 41
0 0
Vikas Sharma (+91-9780449303)
Molecular Modeling lab.
Department of Medicinal Chemistry
National Institute of Pharmaceutical Education & Research (NIPER),
SAS Nagar, Mohali,
Punjab (INDIA)
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Received on Sun Jun 07 2009 - 01:07:12 PDT
