AMBER Archive (2002)

Subject: MD on cytochrome

From: Mahadevan Seetharaman (maha_at_vwl.medc.umn.edu)
Date: Thu Aug 01 2002 - 16:15:52 CDT

HI,

I have just built a homology model of a cyochrome with heme and minimized
it in amber. I was wondering if there is a way to optimize the sidechains
by performing dynamics.

I couldn't use implicit solvent (problem with the heme Fe) and the system
is too big for explicit solvent simulations.

Any suggestions?

Thanx
Mahadevan