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Appendix C: Example Input Files
’wtnoe’ and ’wtvdw’, respectively. The NOE distance constraints are read
from the file ‘conotoxin.noe’.
setmodel
read parm file paramstd.dat noprint
energy parm cutoff 10.0 diel 1.0 distance listupdate 10
print 50
setpotential
mmechanics force noecon name conotoxin all no14 noel nohb
constraint name conotoxin noec dist file conotoxin.noe con1 40 con2 2
weight constraint name conotoxin noe ’wtnoe’
weight intermolecular vdw ’wtvdw’
quit
quit
The system is minimized using the conjugate gradient minimizer. The value
of the table, ’increment’ is used specify the number of cycles of minimization to be performed. The values of the initial and maximum step
sizes as well as the convergence criteria are typical. Coordinate restart and
Brookhaven PDB format files are written after minimization.
minm
conjugate
dx0 0.5 dxm 1.0
input cntl mxcyc ’increment’ rmscut 0.1 deltae 0.0001
run
write restart coordinates formatted file ’rstfile’
write pdb coordinates file ’pdbfile’ name conotoxin
quit
The Lennard-Jones 6-12 component of the system energy is appended to the
table ’energylj612’, and the number minimization cycles is appended to
the table ’mincycles’.
put ’energylj612’ append ’current.lj612’ into ’energylj612’
put ’mincycles’ append ’stepcount’ into ’mincycles’
The values are weighting coefficients are scaled, the loop control variable is
incremented, and the minimization step count is updated.
put ’wtvdw’ * 10.0
into ’wtvdw’
put ’wtnoe’ *
into ’wtnoe’
2.0
put ’stepcount’ + ’increment’ into ’stepcount’
put ’counter’ + 1
into ’counter’
reset ’current.lj612’
endwhile
The result tables ’mincycles’ and ’energylj612’ are printed in the output
file.
table
printoptions title Minimization cycles versus 6-12 energy
FirstDiscovery 3.0 Command Reference Manual
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