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*
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--
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 - 17:00:02 PDT
