Thank you very much. I should take a look at that.
Regards,
Simon
2018-06-11 17:07 GMT+08:00 Stephan Schott <sschottv.gmail.com>:
> Hi Simon,
> I'm not sure what you mean, but the force will be applied to the atoms that
> are in the "iat" section only, and will be relative to the type of
> restraint you are applying. I can recommend you to check the rst command
> from cpptraj; this should make your job a bit easier.
> Cheers,
>
> 2018-06-09 12:29 GMT+02:00 Simon Kit Sang Chu <simoncks1994.gmail.com>:
>
> > Dear Stephan,
> >
> > I did notice &wt frequently appearing but I never expected to use it in
> > distance restraint. I thought one only needed it in heat.in / changing
> > temperature.
> >
> > Meanwhile, does distance restraint apply force on both atoms? If so, is
> > there a way to apply the force only on a particular set of atoms for such
> > restraint? Same for angle and torsional restraint.
> >
> > Thanks.
> >
> > Regards,
> > Simon
> >
> > 2018-06-09 1:16 GMT+08:00 Stephan Schott <schottve.hhu.de>:
> >
> > > 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
> > > > >
> > > > _______________________________________________
> > > > 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
> >
>
>
>
> --
> Stephan Schott V.
> Bioquímico / Licenciado en Bioquímica
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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>
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Received on Mon Jun 11 2018 - 08:30:02 PDT
