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
&cntrl
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
