[AMBER] amber topology file for cytochrome c covalently bond to Heme

From: Shoresh Shafei <shoresh.shafei.duke.edu>
Date: Mon, 6 Jul 2015 17:07:58 +0000

Dear Amber Experts,

I am trying to generate a topology file for pdb ID: 1c52 where histidine and methionine residues are covalently bond to Fe of the heme cofactor. The force field parameters provided by PhD thesis of Giammona has been used for cytochromes (http://www.pharmacy.manchester.ac.uk/bryce/amber/).

When using this force field, I do not get any error, however there is no bond between Fe and NE2 of Histidine and Fe and S of Methionine. Since this force field has been used for a long time, I wonder what other groups have done to establish these bonds. Or maybe I am missing something... I have done literature search online but the result is not much helpful.

I appreciate your comments,
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Received on Mon Jul 06 2015 - 10:30:03 PDT
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