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
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Received on Thu Mar 18 2010 - 07:30:03 PDT
