[AMBER] minimization segmentation fault

From: Jorgen Simonsen <jorgen589.gmail.com>
Date: Thu, 22 Jul 2010 15:16:02 +0200


I am minimization a protein complex where I have decided to keep all the
crystal waters - this might be one of my problems though. I want to start a
minimization of the crystal water

Minimization of water molecules rest is fixed
  imin = 1,
  maxcyc = 50000,
  ncyc = 25000,
  ntb = 0,
  ntr = 1,
  igb = 0,
  cut = 12
Hold protein fixed
RES 1 802

The first of the minimization the energies explode which I presume are due
to bad vdw interaction -clashing I have tried to change the dt=0.00001 but
that did not solve the problem. I would prefer not to remove too many of the
crystal waters but could I try just to minimize the hydrogens in the system?
I have tried selection like

ATOM '!.H'

instead of RES but this is a wrong syntax how to fix this?
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Received on Thu Jul 22 2010 - 06:30:04 PDT
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