Dear Amber users ,
I am trying to equilibrate my system ( HCA2
hydrated)
using PM3 as qm_theory . Now my initial structure and equilibrated
structure
differ a bit. Some crystal water of the initial structure have come out of
the qm- zone during equilibration , while some solvation water have come
into the
qm- zone. Now when I am trying to equilibrate the system taking solvation
water into the qm- zone, convergence is not achieved but when I am taking
only the crystal water , there is no problem in convergence. Can anyone
tell
me whether there are any restrictions in specifying the qm-zone in amber
and
the reasons behind my convergence failure ?
I am using amber12 and I have minimised , heated and then equilibrated my
system with MM first , then tried to go for qm/mm.
Any suggestion will be highly entertained .
With
regards Tanmoy
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Received on Mon Dec 02 2013 - 03:00:02 PST
