I mean as a tool for determining where the problem is, not for your final
data. if it works without the cofactor, then it must be in the coordinates
or parameters of the cofactor. it will help you eliminate other things.
On Thu, Mar 18, 2010 at 10:35 AM, Hyma vathi <hymavathi.niper.gmail.com>wrote:
> But I need the cofactor also because it is present in the active site
>
> On Thu, Mar 18, 2010 at 7:59 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > try without the cofactor- use only standard force fields. see if the
> > problem
> > goes away.
> >
> > On Thu, Mar 18, 2010 at 10:28 AM, Hyma vathi <hymavathi.niper.gmail.com
> > >wrote:
> >
> > > Dear Carlos and Ross,
> > > Thank you for your reply. Now I successfully minimised the protein but
> > when
> > > I subjected it to heating again there was error message which Iam
> posting
> > > below. I am unable to get the problem. I will very greatful if you
> could
> > > help me out with the problem.
> > > And I have another query also, actually I am dealing with a protein
> which
> > > has a cofactor which is creating the problem, I did try to carefully
> > > extract
> > > the cofactor from cocrystal structure and correct the atom and bond
> types
> > > and saved it in a mol2 format and submitted to antechamber but
> everytime
> > > some error regarding its charges arises . Can you please suggest some
> > > solution regarding its charges? Thank you in advance.
> > >
> > > Here is the input file:
> > >
> > > heat
> > > protein
> > > &cntrl
> > >
> > >
> > > imin=0,irest=0,ntx=1,
> > >
> > >
> > > nstlim=25000,dt=0.002,
> > >
> > >
> > > ntf=5,
> > >
> > > cut=8.0,
> > > ntb=1,
> > > ntpr=500,
> > > ntwx=500,
> > > ntt=3,
> > > gamma_ln=2.0,
> > > tempi=0.0,
> > > temp0=300.0,
> > > ntr=1,
> > > restraintmask=':1-317',
> > >
> > > restraint_wt=2.0,
> > >
> > >
> > > nmropt=1
> > >
> > > /
> > >
> > > &wt TYPE='TEMP0', istep1=0,
> > > istep2=25000,
> > > value1=0.1, value2=300.0,
> > > /
> > > &wt TYPE='END'
> > > /
> > >
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > > 1. RESOURCE USE:
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > >
> > > |
> > > Flags:
> > >
> > > getting new box info from bottom of inpcrd
> > > | INFO: Old style inpcrd file read
> > >
> > > | peek_ewald_inpcrd: Box info found
> > > |Largest sphere to fit in unit cell has radius = 32.369
> > > | New format PARM file being parsed.
> > > | Version = 1.000 Date = 03/18/10 Time = 10:20:51
> > > NATOM = 31140 NTYPES = 21 NBONH = 28541 MBONA = 2663
> > > NTHETH = 5871 MTHETA = 3632 NPHIH = 11096 MPHIA = 9021
> > > NHPARM = 0 NPARM = 0 NNB = 63312 NRES = 8979
> > > NBONA = 2663 NTHETA = 3632 NPHIA = 9021 NUMBND = 79
> > > NUMANG = 163 NPTRA = 60 NATYP = 54 NPHB = 1
> > > IFBOX = 1 NMXRS = 73 IFCAP = 0 NEXTRA = 0
> > > NCOPY = 0
> > >
> > >
> > > | Memory Use Allocated
> > > | Real 1704962
> > > | Hollerith 195821
> > > | Integer 1082753
> > > | Max Pairs 10380000
> > > | nblistReal 373680
> > > | nblist Int 1708281
> > > | Total 68453 kbytes
> > > | Duplicated 0 dihedrals
> > > | Duplicated 0 dihedrals
> > >
> > > BOX TYPE: RECTILINEAR
> > >
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > > 2. CONTROL DATA FOR THE RUN
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > >
> > >
> > >
> > >
> > > General flags:
> > > imin = 0, nmropt = 1
> > >
> > > Nature and format of input:
> > > ntx = 1, irest = 0, ntrx = 1
> > >
> > > Nature and format of output:
> > > ntxo = 1, ntpr = 500, ntrx = 1, ntwr =
> > > 500
> > > iwrap = 0, ntwx = 500, ntwv = 0, ntwe
> > > = 0
> > > ioutfm = 0, ntwprt = 0, idecomp = 0,
> > > rbornstat= 0
> > >
> > > Potential function:
> > > ntf = 5, ntb = 1, igb = 0, nsnb =
> > > 25
> > > ipol = 0, gbsa = 0, iesp = 0
> > > dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
> > > scnb = 2.00000, scee = 1.20000
> > >
> > > Frozen or restrained atoms:
> > > ibelly = 0, ntr = 1
> > >
> > > Molecular dynamics:
> > > nstlim = 25000, nscm = 1000, nrespa = 1
> > > t = 0.00000, dt = 0.00200, vlimit = 20.00000
> > >
> > > Langevin dynamics temperature regulation:
> > > ig = 71277
> > > temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
> > >
> > > NMR refinement options:
> > > iscale = 0, noeskp = 1, ipnlty = 1, mxsub
> > > = 1
> > > scalm = 100.00000, pencut = 0.10000, tausw = 0.10000
> > >
> > > Ewald parameters:
> > > verbose = 0, ew_type = 0, nbflag = 1, use_pme
> > > = 1
> > > vdwmeth = 1, eedmeth = 1, netfrc = 1
> > > Box X = 76.965 Box Y = 64.737 Box Z = 79.558
> > > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> > > NFFT1 = 80 NFFT2 = 64 NFFT3 = 80
> > > Cutoff= 8.000 Tol =0.100E-04
> > > Ewald Coefficient = 0.34864
> > > Interpolation order = 4
> > >
> > > LOADING THE CONSTRAINED ATOMS AS GROUPS
> > >
> > >
> > > 5. REFERENCE ATOM COORDINATES
> > >
> > >
> > > Mask :1-317; matches 5164 atoms
> > >
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > > 3. ATOMIC COORDINATES AND VELOCITIES
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > >
> > >
> > >
> > > begin time read from input coords = 0.000 ps
> > >
> > >
> > >
> > > Begin reading energy term weight changes/NMR restraints
> > > WEIGHT CHANGES:
> > > TEMP0 0 25000 0.100000 300.000000 0 0
> > >
> > > RESTRAINTS:
> > > ** No restraint defined **
> > >
> > > Done reading weight changes/NMR restraints
> > >
> > >
> > > Number of triangulated 3-point waters found: 8657
> > >
> > > Sum of charges from parm topology file = -0.00060013
> > > Forcing neutrality...
> > >
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > > 4. RESULTS
> > >
> > >
> >
> --------------------------------------------------------------------------------
> > >
> > > | # of SOLUTE degrees of freedom (RNDFP): 93420.
> > > | # of SOLVENT degrees of freedom (RNDFS): 0.
> > > | NDFMIN = 93420. NUM_NOSHAKE = 0 CORRECTED RNDFP =
> > > 93420.
> > > | TOTAL # of degrees of freedom (RNDF) = 93420.
> > > ---------------------------------------------------
> > > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> > > using 5000.0 points per unit in tabled values
> > > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> > > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> > > | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
> > > ---------------------------------------------------
> > > | Local SIZE OF NONBOND LIST = 5289059
> > > | TOTAL SIZE OF NONBOND LIST = 5289059
> > >
> > > NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> > > 0.0
> > > Etot = -108586.1794 EKtot = 0.0000 EPtot =
> > > -108586.1794
> > > BOND = 0.0000 ANGLE = 0.0000 DIHED =
> > > 3141.3544
> > > 1-4 NB = 1672.2138 1-4 EEL = 14120.0144 VDWAALS =
> > > 18993.4450
> > > EELEC = -146513.2070 EHBOND = 0.0000 RESTRAINT =
> > > 0.0000
> > > Ewald error estimate: 0.7641E-04
> > >
> > >
> >
> ------------------------------------------------------------------------------
> > >
> > > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
> > 0.000
> > >
> > >
> >
> ===============================================================================
> > > vlimit exceeded for step 0; vmax = 25.5333
> > > vlimit exceeded for step 2; vmax = 46.1433
> > > vlimit exceeded for step 3; vmax = 21.0504
> > > vlimit exceeded for step 4; vmax = 77.4041
> > > vlimit exceeded for step 5; vmax = 103.6841
> > > vlimit exceeded for step 6; vmax = 1439.0893
> > > vlimit exceeded for step 7; vmax = 6447.8178
> > > vlimit exceeded for step 8; vmax = 72724.6192
> > > vlimit exceeded for step 9; vmax = 5504.9090
> > > vlimit exceeded for step 10; vmax = 19177.1264
> > > vlimit exceeded for step 11; vmax = **********
> > > vlimit exceeded for step 12; vmax = **********
> > > vlimit exceeded for step 13; vmax = **********
> > > vlimit exceeded for step 14; vmax = **********
> > > vlimit exceeded for step 15; vmax = **********
> > > vlimit exceeded for step 16; vmax = **********
> > > vlimit exceeded for step 17; vmax = **********
> > > vlimit exceeded for step 18; vmax = **********
> > > vlimit exceeded for step 19; vmax = **********
> > > vlimit exceeded for step 20; vmax = **********
> > > vlimit exceeded for step 21; vmax = **********
> > > vlimit exceeded for step 22; vmax = **********
> > > vlimit exceeded for step 23; vmax = **********
> > > vlimit exceeded for step 24; vmax = **********
> > > vlimit exceeded for step 25; vmax = **********
> > > vlimit exceeded for step 26; vmax = **********
> > > vlimit exceeded for step 27; vmax = **********
> > > vlimit exceeded for step 28; vmax = **********
> > > vlimit exceeded for step 29; vmax = **********
> > > vlimit exceeded for step 30; vmax = **********
> > > vlimit exceeded for step 31; vmax = **********
> > > vlimit exceeded for step 32; vmax = **********
> > > vlimit exceeded for step 33; vmax = **********
> > > vlimit exceeded for step 34; vmax = **********
> > > vlimit exceeded for step 35; vmax = **********
> > > vlimit exceeded for step 36; vmax = **********
> > > vlimit exceeded for step 37; vmax = **********
> > > vlimit exceeded for step 38; vmax = **********
> > > vlimit exceeded for step 39; vmax = **********
> > > vlimit exceeded for step 40; vmax = **********
> > > vlimit exceeded for step 41; vmax = **********
> > > vlimit exceeded for step 42; vmax = **********
> > > vlimit exceeded for step 43; vmax = **********
> > > vlimit exceeded for step 44; vmax = **********
> > > vlimit exceeded for step 45; vmax = **********
> > > vlimit exceeded for step 46; vmax = **********
> > > vlimit exceeded for step 47; vmax = **********
> > > vlimit exceeded for step 48; vmax = **********
> > > vlimit exceeded for step 49; vmax = **********
> > > vlimit exceeded for step 50; vmax = **********
> > > vlimit exceeded for step 51; vmax = **********
> > > vlimit exceeded for step 52; vmax = **********
> > > vlimit exceeded for step 53; vmax = **********
> > > vlimit exceeded for step 54; vmax = **********
> > > vlimit exceeded for step 55; vmax = **********
> > > vlimit exceeded for step 56; vmax = **********
> > > vlimit exceeded for step 57; vmax = **********
> > > vlimit exceeded for step 58; vmax = **********
> > > vlimit exceeded for step 59; vmax = **********
> > > vlimit exceeded for step 60; vmax = **********
> > > vlimit exceeded for step 61; vmax = **********
> > > vlimit exceeded for step 62; vmax = **********
> > > vlimit exceeded for step 63; vmax = **********
> > > vlimit exceeded for step 64; vmax = **********
> > > vlimit exceeded for step 65; vmax = **********
> > > vlimit exceeded for step 66; vmax = **********
> > > vlimit exceeded for step 67; vmax = **********
> > > vlimit exceeded for step 68; vmax = **********
> > > vlimit exceeded for step 69; vmax = **********
> > > vlimit exceeded for step 70; vmax = **********
> > > vlimit exceeded for step 71; vmax = **********
> > > vlimit exceeded for step 72; vmax = **********
> > > vlimit exceeded for step 73; vmax = **********
> > > vlimit exceeded for step 74; vmax = **********
> > > vlimit exceeded for step 75; vmax = **********
> > > vlimit exceeded for step 76; vmax = **********
> > > vlimit exceeded for step 77; vmax = **********
> > > vlimit exceeded for step 78; vmax = **********
> > > vlimit exceeded for step 79; vmax = **********
> > > vlimit exceeded for step 80; vmax = **********
> > > vlimit exceeded for step 81; vmax = **********
> > > vlimit exceeded for step 82; vmax = **********
> > > vlimit exceeded for step 83; vmax = **********
> > > vlimit exceeded for step 84; vmax = **********
> > > vlimit exceeded for step 85; vmax = **********
> > > vlimit exceeded for step 86; vmax = **********
> > > vlimit exceeded for step 87; vmax = **********
> > > vlimit exceeded for step 88; vmax = **********
> > > vlimit exceeded for step 89; vmax = **********
> > > vlimit exceeded for step 90; vmax = **********
> > > vlimit exceeded for step 91; vmax = **********
> > > vlimit exceeded for step 92; vmax = **********
> > > vlimit exceeded for step 93; vmax = **********
> > > vlimit exceeded for step 94; vmax = **********
> > > vlimit exceeded for step 95; vmax = **********
> > > vlimit exceeded for step 96; vmax = **********
> > > vlimit exceeded for step 97; vmax = **********
> > > vlimit exceeded for step 98; vmax = **********
> > > vlimit exceeded for step 99; vmax = **********
> > > vlimit exceeded for step 100; vmax = **********
> > > vlimit exceeded for step 101; vmax = **********
> > > vlimit exceeded for step 102; vmax = **********
> > > vlimit exceeded for step 103; vmax = **********
> > > vlimit exceeded for step 104; vmax = **********
> > > vlimit exceeded for step 105; vmax = **********
> > > vlimit exceeded for step 106; vmax = **********
> > > vlimit exceeded for step 107; vmax = **********
> > > vlimit exceeded for step 108; vmax = **********
> > > vlimit exceeded for step 109; vmax = **********
> > > vlimit exceeded for step 110; vmax = **********
> > > vlimit exceeded for step 111; vmax = **********
> > > vlimit exceeded for step 112; vmax = **********
> > > vlimit exceeded for step 113; vmax = **********
> > > vlimit exceeded for step 114; vmax = **********
> > > vlimit exceeded for step 115; vmax = **********
> > > vlimit exceeded for step 116; vmax = **********
> > > vlimit exceeded for step 117; vmax = **********
> > > vlimit exceeded for step 118; vmax = **********
> > > vlimit exceeded for step 119; vmax = **********
> > > vlimit exceeded for step 120; vmax = **********
> > > vlimit exceeded for step 121; vmax = **********
> > > vlimit exceeded for step 122; vmax = **********
> > > vlimit exceeded for step 123; vmax = **********
> > > vlimit exceeded for step 124; vmax = **********
> > > vlimit exceeded for step 125; vmax = **********
> > > vlimit exceeded for step 126; vmax = **********
> > > vlimit exceeded for step 127; vmax = **********
> > > vlimit exceeded for step 128; vmax = **********
> > > vlimit exceeded for step 129; vmax = **********
> > > vlimit exceeded for step 130; vmax = **********
> > > vlimit exceeded for step 131; vmax = **********
> > > vlimit exceeded for step 132; vmax = **********
> > > vlimit exceeded for step 133; vmax = **********
> > > vlimit exceeded for step 134; vmax = **********
> > > vlimit exceeded for step 135; vmax = **********
> > > vlimit exceeded for step 136; vmax = **********
> > > vlimit exceeded for step 137; vmax = **********
> > > vlimit exceeded for step 138; vmax = **********
> > > vlimit exceeded for step 139; vmax = **********
> > > vlimit exceeded for step 140; vmax = **********
> > > vlimit exceeded for step 141; vmax = **********
> > > vlimit exceeded for step 142; vmax = **********
> > > vlimit exceeded for step 143; vmax = 15813.7646
> > > vlimit exceeded for step 144; vmax = **********
> > > vlimit exceeded for step 145; vmax = **********
> > > vlimit exceeded for step 146; vmax = 2119.6107
> > > vlimit exceeded for step 147; vmax = **********
> > > vlimit exceeded for step 148; vmax = **********
> > > vlimit exceeded for step 149; vmax = **********
> > > vlimit exceeded for step 150; vmax = **********
> > > vlimit exceeded for step 151; vmax = 76195.5182
> > > vlimit exceeded for step 152; vmax = **********
> > > vlimit exceeded for step 153; vmax = **********
> > > vlimit exceeded for step 154; vmax = **********
> > > vlimit exceeded for step 155; vmax = **********
> > > vlimit exceeded for step 156; vmax = **********
> > > vlimit exceeded for step 157; vmax = 83437.3616
> > > vlimit exceeded for step 158; vmax = **********
> > > vlimit exceeded for step 159; vmax = **********
> > > vlimit exceeded for step 160; vmax = **********
> > > vlimit exceeded for step 161; vmax = **********
> > > vlimit exceeded for step 162; vmax = **********
> > > vlimit exceeded for step 163; vmax = **********
> > > vlimit exceeded for step 164; vmax = **********
> > > vlimit exceeded for step 165; vmax = **********
> > > vlimit exceeded for step 166; vmax = 21315.3512
> > > vlimit exceeded for step 167; vmax = 33197.2520
> > > vlimit exceeded for step 168; vmax = 42058.2345
> > > vlimit exceeded for step 169; vmax = **********
> > > vlimit exceeded for step 170; vmax = **********
> > > vlimit exceeded for step 171; vmax = 4307.4793
> > > vlimit exceeded for step 172; vmax = **********
> > > vlimit exceeded for step 173; vmax = **********
> > > vlimit exceeded for step 174; vmax = 14646.3685
> > > vlimit exceeded for step 175; vmax = 12999.2123
> > > vlimit exceeded for step 176; vmax = **********
> > > vlimit exceeded for step 177; vmax = 7131.1858
> > > vlimit exceeded for step 178; vmax = 12732.7213
> > > vlimit exceeded for step 179; vmax = **********
> > > vlimit exceeded for step 180; vmax = **********
> > > vlimit exceeded for step 181; vmax = **********
> > > vlimit exceeded for step 182; vmax = **********
> > > vlimit exceeded for step 183; vmax = 2044.7677
> > > vlimit exceeded for step 184; vmax = 19189.0205
> > > vlimit exceeded for step 185; vmax = **********
> > > vlimit exceeded for step 186; vmax = **********
> > > vlimit exceeded for step 187; vmax = 34519.4885
> > > vlimit exceeded for step 188; vmax = 7242.8384
> > > vlimit exceeded for step 189; vmax = 7221.0307
> > > vlimit exceeded for step 190; vmax = 56688.5761
> > > vlimit exceeded for step 191; vmax = 1235.0009
> > > vlimit exceeded for step 192; vmax = 25898.1064
> > > vlimit exceeded for step 193; vmax = **********
> > > vlimit exceeded for step 194; vmax = 12428.1251
> > > vlimit exceeded for step 195; vmax = **********
> > > vlimit exceeded for step 196; vmax = 3939.7656
> > > vlimit exceeded for step 197; vmax = 1708.0617
> > > vlimit exceeded for step 198; vmax = 16276.7790
> > > vlimit exceeded for step 199; vmax = 1704.5026
> > > vlimit exceeded for step 200; vmax = 338.8856
> > > vlimit exceeded for step 201; vmax = **********
> > > vlimit exceeded for step 202; vmax = 35.1344
> > > vlimit exceeded for step 203; vmax = **********
> > > vlimit exceeded for step 204; vmax = **********
> > > vlimit exceeded for step 205; vmax = 556.3115
> > > vlimit exceeded for step 206; vmax = 345.6561
> > > vlimit exceeded for step 207; vmax = 338.4137
> > > vlimit exceeded for step 208; vmax = 224.4256
> > > vlimit exceeded for step 209; vmax = **********
> > > vlimit exceeded for step 210; vmax = 117.8948
> > > vlimit exceeded for step 211; vmax = 46.0596
> > > vlimit exceeded for step 212; vmax = 104.8180
> > > vlimit exceeded for step 213; vmax = **********
> > > vlimit exceeded for step 214; vmax = 104.7114
> > > vlimit exceeded for step 215; vmax = 20.7017
> > > vlimit exceeded for step 216; vmax = 3688.0894
> > > vlimit exceeded for step 217; vmax = 407.1374
> > > vlimit exceeded for step 218; vmax = 27.9654
> > > vlimit exceeded for step 219; vmax = 33.0142
> > > vlimit exceeded for step 220; vmax = 59.5361
> > > vlimit exceeded for step 221; vmax = 7185.4351
> > > vlimit exceeded for step 222; vmax = 95471.5188
> > > vlimit exceeded for step 223; vmax = 22.4600
> > > vlimit exceeded for step 224; vmax = **********
> > > vlimit exceeded for step 225; vmax = 798.5610
> > > vlimit exceeded for step 226; vmax = **********
> > > vlimit exceeded for step 227; vmax = 893.6647
> > > vlimit exceeded for step 228; vmax = 20.2948
> > > vlimit exceeded for step 229; vmax = 20.0582
> > > vlimit exceeded for step 230; vmax = 318.8326
> > > vlimit exceeded for step 231; vmax = 27.4438
> > > vlimit exceeded for step 232; vmax = 838.8414
> > > vlimit exceeded for step 233; vmax = 75.2698
> > > vlimit exceeded for step 235; vmax = 1554.3386
> > > vlimit exceeded for step 236; vmax = 15859.9992
> > > vlimit exceeded for step 237; vmax = 23.9949
> > > vlimit exceeded for step 238; vmax = 34.1518
> > > vlimit exceeded for step 239; vmax = 471.8508
> > > vlimit exceeded for step 240; vmax = 522.9213
> > > vlimit exceeded for step 241; vmax = 848.8227
> > > vlimit exceeded for step 242; vmax = 510.9438
> > > vlimit exceeded for step 243; vmax = 1649.7875
> > > vlimit exceeded for step 244; vmax = 510.8416
> > > vlimit exceeded for step 245; vmax = 515.2433
> > > vlimit exceeded for step 246; vmax = 510.9043
> > > vlimit exceeded for step 247; vmax = 510.7375
> > > vlimit exceeded for step 248; vmax = 683.9241
> > > vlimit exceeded for step 249; vmax = 510.6138
> > > vlimit exceeded for step 250; vmax = 486.3052
> > > vlimit exceeded for step 251; vmax = **********
> > > vlimit exceeded for step 252; vmax = 533.4413
> > > vlimit exceeded for step 253; vmax = **********
> > > vlimit exceeded for step 254; vmax = 24.5471
> > > vlimit exceeded for step 255; vmax = **********
> > > vlimit exceeded for step 256; vmax = 3313.2506
> > > vlimit exceeded for step 257; vmax = 35.0561
> > > vlimit exceeded for step 258; vmax = 48.5767
> > > vlimit exceeded for step 259; vmax = 150.9836
> > > vlimit exceeded for step 260; vmax = 22.2896
> > > vlimit exceeded for step 261; vmax = 239.5096
> > > vlimit exceeded for step 262; vmax = 21.9114
> > > vlimit exceeded for step 263; vmax = 65.0393
> > > vlimit exceeded for step 264; vmax = 29.8799
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
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> > >
> > _______________________________________________
> > AMBER mailing list
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> >
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>
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Received on Thu Mar 18 2010 - 08:00:05 PDT
