AMBER Archive (2002)

Subject: Escaping Atoms

From: ch cureton (charlie_at_pugh.bip.bham.ac.uk)
Date: Wed Sep 04 2002 - 05:43:03 CDT

I am currently experiencing problems trying to minimise just the waters of
a solvateOct that surrounds a protein. During minimisation the protein has
been restrained but consistently I get escaping atoms problems. I have
increased the closeness value to 3.5 as I thought the waters might be
being expelled due to being to close to the solute. Unfortunately this
course of action has not helped and I would be very grateful for any ideas
as to get around this problem. I am currently using AMBER 6.0 and am using
sander_classic for the minimisation. The mdin I am using is:
 &cntrl
  imin=1,
  maxcyc=100000,
  cut=8.0, scee=1.2,
  ntb=1,
  ntr=1,
  ntpr=100,
  ncyc=5000,
 &end
Group atoms for restraining chym
 5.0
RES 1 237
END
END

Thank you once again
Charly