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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Received on Mon Oct 09 2017 - 17:00:02 PDT
