AMBER Archive (2009)

Subject: [AMBER] Syntax Bellymask

From: Brothers, Michael Charles (mcbroth_at_sandia.gov)
Date: Fri Jul 10 2009 - 18:59:01 CDT

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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