Hi again,
You are missing a section at the end of the input (&wt). For examples,
please take a look at the following tutorials:
http://ambermd.org/Questions/constraints.html
http://ambermd.org/tutorials/advanced/tutorial4/index.htm
http://ambermd.org/tutorials/advanced/tutorial17/index.htm
Also please search the mailing list and the amber manual; there are many
applications that use the same syntax.
Hope it helps,
2018-06-08 16:31 GMT+02:00 Simon Kit Sang Chu <simoncks1994.gmail.com>:
> 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
> > >>>
> > >>
> > >> _______________________________________________
> > >> 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
> > >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> 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
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Received on Fri Jun 08 2018 - 10:30:03 PDT
