[AMBER] Metal parametrization problem!!

From: Pedro A. Baldera Aguayo <a.baldera7.gmail.com>
Date: Fri, 1 Aug 2014 13:17:24 -0500


I'm a totally newbie in Amber. I'm facing some problems when trying to
build the topology files for a Zn metalloprotein, which is connected
bounded to 3 histidines (I have already from HIS to HID), 1 aspartate and 2
water molecules. I've tried to following your comments according this post
http://archive.ambermd.org/201406/0518.html; however:

1. I do not how to add the Hydrogens to the water molecules via tleap

2. Do I need to change HOH to MOH for the 2 molecules that are bounded to
the Zn in order to be recognized for MCPB? Is this mandatory? It is a

I would really appreciate your help, thanks in advance for your time

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Received on Fri Aug 01 2014 - 11:30:03 PDT
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