[AMBER] instablity of ligand during minimization

From: Ibrahim Said <saidibrahim569.gmail.com>
Date: Tue, 9 Jul 2013 23:09:15 +0300

Dear Amber users
I am running QM/MM experiment for a schiff base. My system is composed of
fructopyranose attached to an Nepsilon of lysine residue in my protein. I
ran minimization for this system in two steps. The first for water and the
second for whole system. The pdb file extracted for first minimization is
OK, but the pdb file derived from minimization for whole system displayed
an opened ring for fructose and I tried to find out the reason(s) but I
could not. Please I attached my namelist for whole system. Any suggestions
will be appreciated.
best wishes,


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Received on Tue Jul 09 2013 - 13:30:02 PDT
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