[AMBER] problem in minimization

From: Carlos Romero <carlos.rom.74he.gmail.com>
Date: Mon, 20 Nov 2017 01:16:28 -0600

Hi dear AMBER users:

I try to make a MD for a complex (602 residues), but when I heat it, it
does not work, appears the following:
 Note: This is usually a symptom of some deeper
     problem with the energetics of the system.
I understand that it is because of some atoms are overlapping,
I analyzed coordinates from crystallographic structure and I found many
overlapped coordinates, but they do not disappear with minimization.
I started with the following min.in
  imin = 1,
  maxcyc = 2500,
  ncyc = 1000,
  ntb = 1,
  ntr = 0,
  cut = 8

I did three consecutive minimizations and problem persist.
I would appreciate any suggestion.

Thanks in advance.
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Received on Sun Nov 19 2017 - 23:30:02 PST
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