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
> >
>
>
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>
--
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 - 05:00:02 PDT
