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
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Received on Fri Jun 08 2018 - 04:30:02 PDT
