It is usually considered acceptable, although the message "failure"
sounds a bit alarming. What it means is that the minimizer does not want
to waste your CPU time anymore and it implicitly advices you that it is
time to use your CPUs for other more interesting things (e.g., start
MD), albeit in a somewhat blunt way. One thing you can do is to set
minimization steps to 200 (two hundred).
Good luck!
yong
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of S.Sundar Raman
Sent: Wednesday, April 13, 2005 12:00 AM
To: amber.scripps.edu
Subject: AMBER: freee energy calculation without minimised structure
dear all,
i am working on peptide conformations in various secondrary structure.
in that i build a model squence as like collagen as gly-pro-hyp. i want
to calculate free energy of that system. when i minimised that model it
never ended normally, it always ended in repeated laminin failure.is it
ok to start free energy calculation with laminin failure structre. or
what i have to do to get rid of laminin failure. thanks
--
S.Sundar Raman
Chemical Lab,
CLRI
Chennai-20
ph: 044-24411830
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Received on Wed Apr 13 2005 - 08:53:00 PDT
