AMBER Archive (2009)

Subject: [AMBER] Heme + Fe(II) + O2 + histidine parameter

From: Haining Liu (
Date: Wed Sep 02 2009 - 22:36:31 CDT


I want to run a MD simulation on hemoglobin. My question is how to get
the parameter for heme? From a literature search, people seem to
consider the (heme + O2 + Fe(II) + histidine) as a whole residue and
calculate the RESP charge using the Gaussian program. However, if such a
system is used in Gaussian, the histidine residue is not complete, i.e.,
its backbone is cut from crystal structure. In that case, how can I
determine the total charge of the system in order to run the quantum
calculation? The second question is how to let the AMBER program know
that the histdine should be included in heme? Do I have to modify the
PDB file?

Thanks very much.

Haining Liu

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