With pmemd (i.e., I can't use restraintmask) in Amber10 the following
heat5.in file
Heating gradually under GB conditions
with restraint on Cl-
Then continuing equilibration at 300K.
&cntrl
imin=0, irest=0, ntx=1, ntb=0,
igb=5, ntc=2, ntf=2,
ntt=3, gamma_ln=2.0,
nstlim=3000, dt=0.002,
ntpr=100, ntwx=100,
tempi=290.0, temp0=300.0,
cut=999.0, rgbmax=999.0,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=600,
value1=290.0, value2=300.0,
/
&wt TYPE='END'
/
Keep Cl- 427 restrained
32.0
RES 427
END
END
(actually there are several other C-, same layout)
did not succeed in imposing positional restraints, as from the out file:
begin time read from input coords = 10.000 ps
Begin reading energy term weight changes/NMR restraints
WEIGHT CHANGES:
TEMP0 0 600 290.000000 300.000000 0 0
RESTRAINTS:
No valid redirection requests found
** No restraint defined **
Done reading weight changes/NMR restraints
In previous procedure heat4.in (from which heat4.rst was used to
launch this procedure) there was no positional restraint. Does ""No
valid redirection" mean that positional restraint should be placed
before weigth restraint?
Thanks
francesco pietra
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Received on Fri Dec 05 2008 - 15:46:02 PST
