[gmx-users] Fwd: HEME-cysteine gromacs simulation

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 7 15:59:44 CEST 2012


Please send requests for help to the gmx-users mailing list. I (and most 
others there) are not available as private tutors.

Contrary to your assertion below, I've never run any simulations on 
cytochrome P450. You probably need to name your iron atom more suitably 
for your force field to recognize (if it can).


-------- Original Message --------
Subject: 	HEME-cysteine gromacs simulation
Date: 	Mon, 07 May 2012 21:04:05 +0800
From: 	Bing Zhang <mpezb310 at gmail.com>
To: 	mark.abraham at anu.edu.au

Dear Mr. Abraham:

This is Zhang Bing, from National University of Singapore, writing to 
bother you for your kind help. I am running into some problems you had a 
couple years ago when running cytochrom P450 MD simulations:
http://lists.gromacs.org/pipermail/gmx-users/2009-August /044495.html . 
The iron Fe in my cytochrome C is also recognized as Fluorine after run 
pdb2gmx. I tried so many ways and hope to get the problem solved, 
unfortunately, failed. I was wondering whether you could kindly give 
some clues how you solved your problems. I hope the email won't take you 
too much time, considering it is a quite "old" question.

I have been stuck  for a while and my research is now pending here, so 
any suggestions or advice from you will be greatly greatly appreciated.

With best regards,

Zhang Bing

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