I tried Stephen's suggestion. Removing the comment and setting "nmropt = 1"
outputs a new error -
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ACE
begin time read from input coords = 20.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
ERROR: No "wt" namelist with TYPE=END found
I did not know distance restraint is a NMR restraint and requires
nmropt setting.
Regards,
Simon
2018-06-08 20:42 GMT+08:00 Bill Ross <ross.cgl.ucsf.edu>:
> That would be a minimal reason. Beyond that, the solution as mentioned
> by Stephan Schott,
>
> > I see a exclamation mark in front of nmropt, which in practice is as
> having nmropt = 0.
>
> !nmropt = 1, ! read extra restraint input from external
>
> Bill
>
>
>
> On 6/8/18 5:22 AM, Simon Kit Sang Chu wrote:
> > Hi Bill,
> >
> > Yes. I think I am pointing the correct input file.
> >
> > Regards,
> > Simon
> >
> > 2018-06-08 20:18 GMT+08:00 Bill Ross <ross.cgl.ucsf.edu>:
> >
> >>> Indeed, there was no energy in restraint part. I should have checked
> that
> >>> earlier. But where exactly I missed in the input file?
> >> Does your cmdline arg point to the right mdin?
> >>
> >> Bill
> >>
> >> On 6/8/18 4:50 AM, Simon Kit Sang Chu wrote:
> >>> Dear all,
> >>>
> >>> Thanks for all your prompt reply. This is a section of the output file.
> >>>
> >>> ------------------------------------------------------------
> >> --------------------
> >>> 2. CONTROL DATA FOR THE RUN
> >>> ------------------------------------------------------------
> >> --------------------
> >>> ACE
> >>>
> >>>
> >>> General flags:
> >>> imin = 0, nmropt = 0
> >>>
> >>> Nature and format of input:
> >>> ntx = 5, irest = 1, ntrx = 1
> >>>
> >>> Nature and format of output:
> >>> ntxo = 2, ntpr = 100, ntrx = 1, ntwr
> =
> >>> 500000
> >>> iwrap = 0, ntwx = 10000, ntwv = 0, ntwe
> =
> >>> 0
> >>> ioutfm = 1, ntwprt = 0, idecomp = 0,
> rbornstat=
> >>> 0
> >>>
> >>> Potential function:
> >>> ntf = 2, 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 = 0
> >>>
> >>> Molecular dynamics:
> >>> nstlim = 500000, nscm = 1000, nrespa = 1
> >>> t = 0.00000, dt = 0.00200, vlimit = 20.00000
> >>>
> >>> Langevin dynamics temperature regulation:
> >>> ig = 695414
> >>> temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
> >>>
> >>> 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 = 100
> >>>
> >>> Ewald parameters:
> >>> verbose = 0, ew_type = 0, nbflag = 1,
> use_pme =
> >>> 1
> >>> vdwmeth = 1, eedmeth = 1, netfrc = 1
> >>> Box X = 30.530 Box Y = 30.530 Box Z = 30.530
> >>> Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> >>> NFFT1 = 32 NFFT2 = 32 NFFT3 = 32
> >>> Cutoff= 8.000 Tol =0.100E-04
> >>> Ewald Coefficient = 0.34864
> >>> Interpolation order = 4
> >>> .
> >>> .
> >>> .
> >>> ------------------------------------------------------------
> >> --------------------
> >>> 4. RESULTS
> >>> ------------------------------------------------------------
> >> --------------------
> >>> ---------------------------------------------------
> >>> 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 = 0.8332E-11 at 2.782960
> >>> ---------------------------------------------------
> >>> |---------------------------------------------------
> >>> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> >>> | with 50.0 points per unit in tabled values
> >>> | Relative Error Limit not exceeded for r .gt. 2.47
> >>> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> >>> | with 50.0 points per unit in tabled values
> >>> | Relative Error Limit not exceeded for r .gt. 2.89
> >>> |---------------------------------------------------
> >>>
> >>> NSTEP = 100 TIME(PS) = 20.200 TEMP(K) = 292.28
> PRESS =
> >>> -1022.8
> >>> Etot = -4181.4073 EKtot = 1010.0270 EPtot =
> >>> -5191.4343
> >>> BOND = 3.0503 ANGLE = 24.7990 DIHED =
> >>> 30.8835
> >>> 1-4 NB = 8.0855 1-4 EEL = 101.2710 VDWAALS =
> >>> 737.2717
> >>> EELEC = -6096.7954 EHBOND = 0.0000 RESTRAINT =
> >>> 0.0000
> >>> EKCMT = 490.7048 VIRIAL = 968.7697 VOLUME =
> >>> 21647.4104
> >>> Density =
> >>> 0.7980
> >>> Ewald error estimate: 0.1519E-03
> >>> ------------------------------------------------------------
> >> ------------------
> >>>
> >>> NSTEP = 200 TIME(PS) = 20.400 TEMP(K) = 307.70
> PRESS =
> >>> -622.6
> >>> Etot = -4156.1706 EKtot = 1063.3369 EPtot =
> >>> -5219.5076
> >>> BOND = 9.5860 ANGLE = 19.8155 DIHED =
> >>> 29.8152
> >>> 1-4 NB = 7.1849 1-4 EEL = 98.2946 VDWAALS =
> >>> 760.9049
> >>> EELEC = -6145.1087 EHBOND = 0.0000 RESTRAINT =
> >>> 0.0000
> >>> EKCMT = 518.2475 VIRIAL = 806.5117 VOLUME =
> >>> 21442.3978
> >>> Density =
> >>> 0.8057
> >>> Ewald error estimate: 0.8508E-04
> >>> ------------------------------------------------------------
> >> ------------------
> >>>
> >>> Indeed, there was no energy in restraint part. I should have checked
> that
> >>> earlier. But where exactly I missed in the input file?
> >>>
> >>> I am not sure if there was a tutorial on how to apply restraints. I am
> >>> current learning by taking a complicated example on page 532 and the
> >>> command explanations in AMBER 2018 manual. I hope there would be more
> >>> intuitive way to learn distance and plane-point restraints.
> >>>
> >>> Regards,
> >>> Simon
> >>>
> >>> 2018-06-08 19:40 GMT+08:00 Stephan Schott <schottve.hhu.de>:
> >>>
> >>>> Hi,
> >>>> Is that exactly the input file you used? Because I see a exclamation
> >> mark
> >>>> in front of nmropt, which in practice is as having nmropt = 0. When
> >>>> restraints are correctly used there is a report of the parsing in the
> >>>> output header, and restraint energies are reported additionally to the
> >>>> usual energies.
> >>>> Hope it helps,
> >>>>
> >>>> 2018-06-08 13:32 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> >>>>
> >>>>> What does the output file show of the restraint input? Copy/paste,
> >>>> please.
> >>>>> Bill
> >>>>>
> >>>>>
> >>>>> On 6/8/18 4:13 AM, Simon Kit Sang Chu wrote:
> >>>>>> Dear AMBER users,
> >>>>>>
> >>>>>> I am new to AMBER usage and I am trying to learn restraints in AMBER
> >>>>>> simulation. I made a simple run on two peptides (ACE-ALA-NME and
> >>>>>> ACE-PRO-NME) solvated. I am trying to set up distance restraint
> >> between
> >>>>> the
> >>>>>> two atoms in the corresponding peptide.
> >>>>>>
> >>>>>> Despite the setting, the trajectory showed that the restraint was
> not
> >>>>>> working. Would anyone mind to point out the missing part in the
> input
> >>>>> file?
> >>>>>> &cntrl
> >>>>>> imin = 0, ! no minimisation
> >>>>>> ntx = 5, ! restart with coordinate and velocity
> >>>>>> irest = 1, ! restart, which means velocity is
> expected
> >> in
> >>>>>> inpcrd
> >>>>>> nstlim = 500000,! number of steps (1 ns)
> >>>>>> dt = 0.002, ! step size
> >>>>>> ntf = 2, ! not to calculate force for SHAKE
> >> constrained
> >>>>> bonds
> >>>>>> ntc = 2, ! SHAKE for all hydrogen-bonded
> >>>>>> temp0 = 300.0 ! temperature
> >>>>>> ntpr = 100, ! info frequency
> >>>>>> ntwx = 10000, ! trajectory frequency
> >>>>>> cut = 8.0, ! cutoff
> >>>>>> ntb = 2, ! PBC for constant pressure
> >>>>>> ntp = 1, ! Berendsen barostat
> >>>>>> ntt = 3, ! Langevin thermostat
> >>>>>> gamma_ln=2.0, ! Langevin thermostat frequency
> >>>>>> ig = -1, ! random seed
> >>>>>> !nmropt = 1, ! read extra restraint input from
> external
> >>>>> DISANG
> >>>>>> file
> >>>>>> /
> >>>>>>
> >>>>>> &rst ! Distance restraint between index 18 23, gradually
> >> increasing
> >>>>> in
> >>>>>> time
> >>>>>> iat = 18, 23, ! iat nonzero up to two
> >>>> scalar >
> >>>>>> distance restraint
> >>>>>> nstep1 = 1, nstep2 = 500000, ! linear scaling of
> >> restraint
> >>>> in
> >>>>>> time
> >>>>>> iresid = 0, ! selecting atoms
> instead of
> >>>>> groups
> >>>>>> (default)
> >>>>>> ifvari = 1, ! time-dependent
> restraint
> >>>>>> coefficient
> >>>>>> ! potential form : 0--linear--r1--harmonic--r2--
> >>>>>> flat--r3--harmonic--r4
> >>>>>> r1 = 0., r2 = 1., r3 = 1., r4 = 99., rk2 = 0., rk3 = 0.,
> >>>>>> r1a= 0., r2a= 1., r3a= 1., r4a= 99., rk2a= 5., rk3a= 5.,
> >>>>>> /
> >>>>>>
> >>>>>> Thanks for your help.
> >>>>>>
> >>>>>>
> >>>>>> Regards,
> >>>>>> Simon
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
> >>>>> AMBER.ambermd.org
> >>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>
> >>>>
> >>>> --
> >>>> Stephan Schott Verdugo
> >>>> Biochemist
> >>>>
> >>>> Heinrich-Heine-Universitaet Duesseldorf
> >>>> Institut fuer Pharm. und Med. Chemie
> >>>> Universitaetsstr. 1
> >>>> 40225 Duesseldorf
> >>>> Germany
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >> _______________________________________________
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> >>
> > _______________________________________________
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> >
>
>
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Received on Fri Jun 08 2018 - 08:00:02 PDT
