Dear Amber members,
I performed SMD simulations to pull out an ion(atom 7536) from the protein active site along a tunnel . I ued the distance of the ion and three atoms of tunnel mouth as RC.I found that the output files are empty.
I dont know what's wrong.Below are input files.
The distance restraint file£º
&rst
iat=com(1035,3374,5917),7356,
r2=11.4,
r2a=9.9,
rk2=7.2,
&end# The first one I tested.
&rst
iat=-1,0
igr1=1035,3374,5917,
igr2=7356
r2=11.4,
r2a=9.9,
rk2=7.2,
&end# The second one I tested.
SMD input file:
30 &cntrl
31 irest = 1, ntx = 5,
32 ntb = 2, pres0 = 1.0, ntp = 1,
33 taup = 2.0,
34 cut = 10.0,
35 ntc = 2, ntf = 2,
36 tempi = 300.0, temp0 = 300.0,
37 ntt = 3, gamma_ln = 2.0,
38 nstlim = $mdsteps, dt = 0.002,
39 ntwx = 1000, ntwr =20000, ntpr = 1000,
40 ig=-1, ioutfm=1,
41 irest = 0, jar=1,
42 /
43 &wt type='DUMPFREQ', istep1=1000 /
44 &wt type='END' /
45 DISANG=dist.RST.dat.1
46 DUMPAVE=asmd_$counter.work.dat.$stage
47 LISTIN=POUT
48 LISTOUT=POUT
I will very appreciate if anyone can offer some suggestions.
Look forward to your reply!
Best wishes.
wjli
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Received on Sun Apr 10 2016 - 05:30:03 PDT
