Dear Gromacs users,
I am planing to do MD of an enzyme that has a Zn in its active site. Up
to now I have used QM/MM or ONIOM approaches but now I need to perform a
long MD and would like to model the Zn with MM, preferably in OPLS.
I know that there are three possible approaches: Bonded, nonbonded and
cationic dummy atom. I have seen a thread, where Maik Goette said that
onyl the bonded approach worked. I would like to know in more detail
what kind of problems could I encounter. What does "not work" imply?
Weeks of unreliable calculations...?
I would also be very grateful if people working in this area could send
me some reference publications, in particular of what can be done with
Gromacs. I have only found: "Zinc binding in proteins and solution: A
simple but accurate nonbonded representation" Roland H. Stote, Martin
Karplus, 1995.
Thanks in advance,
Ramon
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