Hi Adrian,
I used packmol to solvate the box then i added the dimensions to the inpcrd
file
Sanaa
On Mon, Oct 9, 2017 at 5:48 PM Adrian Roitberg <roitberg.ufl.edu> wrote:
> The error is clearly listed as:
>
>
> *| ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not
> supported! Input errors occurred. Terminating execution.*
>
> You have ntb=2, ntp=1 so the problem has to come from ifbox==0 meaning
> that your prmtop does not know anything about a box. How did you solvate it?
> adrian
>
>
> On 10/9/17 7:44 PM, Sanaa ALAbbad wrote:
> > Hi AMBERs,
> >
> > I am running MD simulation of Ru complex in a box of 95% ethanol and
> NH4Cl
> > as counter ion. I generated inpcrd and prmtop files with tleap with the
> > desired concentration. The minimization steps went fine but at the
> > equilibration step the calculations stopped with error:
> > :
> > :
> > :
> > 2. CONTROL DATA FOR THE RUN
> >
> --------------------------------------------------------------------------------
> > default_name
> >
> > General flags:
> > imin = 0, nmropt = 0
> > Nature and format of input:
> > ntx = 1, irest = 0, ntrx = 1
> > Nature and format of output:
> > ntxo = 2, ntpr = 50, ntrx = 1, ntwr =
> > 500
> > iwrap = 1, ntwx = 1000, ntwv = 0, ntwe
> > = 0
> > ioutfm = 1, ntwprt = 0, idecomp = 0,
> > rbornstat= 0
> > Potential function:
> > ntf = 1, ntb = 2, igb = 0, nsnb
> > = 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 1
> > restraint_wt = 4.00000
> > Molecular dynamics:
> > nstlim = 10000, nscm = 0, nrespa = 1
> > t = 0.00000, dt = 0.00100, vlimit = 20.00000
> > Berendsen (weak-coupling) temperature regulation:
> > temp0 = 100.00000, tempi = 298.00000, tautp = 1.00000
> > Pressure regulation:
> > ntp = 1
> > pres0 = 1.00000, comp = 44.60000, taup = 1.00000
> > SHAKE:
> > ntc = 2, jfastw = 0
> > tol = 0.00001
> > ntx = 1, irest = 0, ntrx = 1
> > Nature and format of output:
> > ntxo = 2, ntpr = 50, ntrx = 1, ntwr =
> > 500
> > iwrap = 1, ntwx = 1000, ntwv = 0, ntwe
> > = 0
> > ioutfm = 1, ntwprt = 0, idecomp = 0,
> > rbornstat= 0
> > Potential function:
> > ntf = 1, ntb = 2, igb = 0, nsnb
> > = 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut = 8.00000, intdiel = 1.00000
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 1
> > restraint_wt = 4.00000
> > Molecular dynamics:
> > nstlim = 10000, nscm = 0, nrespa = 1
> > t = 0.00000, dt = 0.00100, vlimit = 20.00000
> > Berendsen (weak-coupling) temperature regulation:
> > temp0 = 100.00000, tempi = 298.00000, tautp = 1.00000
> > Pressure regulation:
> > ntp = 1
> > pres0 = 1.00000, comp = 44.60000, taup = 1.00000
> > SHAKE:
> > ntc = 2, jfastw = 0
> > tol = 0.00001
> > | Intermolecular bonds treatment:
> > | no_intermolecular_bonds = 1
> > | Energy averages sample interval:
> > | ene_avg_sampling = 50
> > Ewald parameters:
> > verbose = 0, ew_type = 0, nbflag = 1, use_pme
> > = 1
> > vdwmeth = 1, eedmeth = 1, netfrc = 1
> > Box X = 107.318 Box Y = 106.882 Box Z = 104.593
> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
> > NFFT1 = 108 NFFT2 = 108 NFFT3 = 108
> > Cutoff= 8.000 Tol =0.100E-04
> > Ewald Coefficient = 0.34864
> > Interpolation order = 4
> > | PMEMD ewald parallel performance parameters:
> > | block_fft = 0
> > | fft_blk_y_divisor = 2
> > | excl_recip = 0
> > | excl_master = 0
> > | atm_redist_freq = 320
> >
> > *| ERROR: the combination ntb != 0, ntp != 0, ifbox == 0 is not
> > supported! Input errors occurred. Terminating execution.*
> >
> > I checked the validity of prmtop and inpcrd using parmed
> >
> >
> > *ParmWarning: ATOMS_PER_MOLECULE section corrupt! Molecules are not
> > contiguous! *
> > So I tried to fix the topology file by running
> > *setMolecules ATOMS_PER_MOLECULE=true*
> >
> >
> >
> >
> > *Setting MOLECULE properties of the prmtop (SOLVENT_POINTERS and
> > ATOMS_PER_MOLECULE)AmberWarning: Molecule atoms are not contiguous! I am
> > attempting to reorder the atoms to fix this.AmberWarning: Residues cannot
> > be part of 2 molecules! Molecule section will not be correctly set.
> > [Offending residue is 10782: <Residue Rud[10782]>]*
> > the Rud is the residue-name of Ru complex.
> > and I named the rest of residues as WAT, EOH, NH4, Cl
> >
> >
> >
> > *What is the appropriate way to fix this error.*
> >
> > *thanks for any help!*
> >
> > *Sanaa Al Abbad*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=JAg-KQEjdZeg_E8PHDDoaw&m=TSKVokz4qdsD3NiYBLmaXd68nqZwZBQ87tpTngTOpQw&s=dqTCpdWewZrvX1rgoBfB2SGysXe-C9dQnIb4BUTJ6cg&e=
>
> --
> Dr. Adrian E. Roitberg
> University of Florida Research Foundation Professor
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
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Received on Mon Oct 09 2017 - 17:00:03 PDT
