you also need to define a box, adding the coordinates only works if the
prmtop knows that it is a periodic system. see the addbox command in leap,
for example.
On Mon, Oct 9, 2017 at 7:52 PM, Sanaa ALAbbad <salabbad79.gmail.com> wrote:
> 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.
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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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> > AMBER.ambermd.org
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> >
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Received on Mon Oct 09 2017 - 17:00:03 PDT
