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
> > > >
> > > _______________________________________________
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> > > 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
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Received on Mon Jun 11 2018 - 02:30:02 PDT
