Hey Amber users
For sander, I'm using the following script for Amber 9 to hold the backbone atoms in place using bellymask. Unfortunately it only appears to be holding atoms 7-21 in place. I've tried colon, space, ., &, etc. in between but have had no luck yet (per advice of the manual. Could anyone provide me the correct syntax?
Thanks,
Mike
Rigid Backbone Amino Acids& 100ps MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0, ibelly = 1,
cut = 10, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 50000, dt = 0.002,
bellymask = .7-21&28-31&38-55&62-65&72-75&82-85&92-95&102-117&124-127&134-137&144-147&154-158&165-168&175-178&185-188&195-198&205-213&220-223&230-233&240-244&248-2344,
ntpr = 100, ntwx = 100, ntwr = 1000
/
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Received on Sat Jul 11 2009 - 01:10:44 PDT
