AMBER Archive (2009)

Subject: [AMBER] How to fix specific atoms? (not residue)

From: Myeong Lee (
Date: Sat Jul 11 2009 - 06:46:06 CDT


I want to hold the specific atoms (not the residues) during minimization
process. I don't know what's the keyword for giving restraint for
specific ATOMS. In other words, I want to fix only part of the atoms in
the same residue.

Another option in case I can't fix individual atoms is to hold the atoms
with atom type "CA". I tried the following, but didn't work. (These
are the atoms which do not belong to DNA/counterion/water)
  imin = 1,
  maxcyc = 4,
  ncyc = 1,
  ntb = 1,
  ntr = 1,
  cut = 10.0
  ntwx = 100


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