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 = **********
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> > _______________________________________________
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> >
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Received on Thu Mar 18 2010 - 08:00:04 PDT
