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 = **********
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> vlimit exceeded for step 30; vmax = **********
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> vlimit exceeded for step 36; vmax = **********
> vlimit exceeded for step 37; vmax = **********
> vlimit exceeded for step 38; vmax = **********
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> vlimit exceeded for step 41; vmax = **********
> vlimit exceeded for step 42; vmax = **********
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> vlimit exceeded for step 46; vmax = **********
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> vlimit exceeded for step 49; vmax = **********
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> vlimit exceeded for step 53; vmax = **********
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> vlimit exceeded for step 55; vmax = **********
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> 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 = **********
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> vlimit exceeded for step 77; vmax = **********
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> 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 = **********
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> vlimit exceeded for step 97; vmax = **********
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> vlimit exceeded for step 117; vmax = **********
> vlimit exceeded for step 118; vmax = **********
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> vlimit exceeded for step 120; vmax = **********
> vlimit exceeded for step 121; vmax = **********
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> vlimit exceeded for step 143; vmax = 15813.7646
> vlimit exceeded for step 144; vmax = **********
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> vlimit exceeded for step 146; vmax = 2119.6107
> vlimit exceeded for step 147; vmax = **********
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> vlimit exceeded for step 151; vmax = 76195.5182
> vlimit exceeded for step 152; vmax = **********
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> vlimit exceeded for step 157; vmax = 83437.3616
> vlimit exceeded for step 158; vmax = **********
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> 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
> _______________________________________________
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>
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Received on Thu Mar 18 2010 - 08:00:02 PDT
