[AMBER] Water coordinated with transition metal

From: ashwini gupta <wini657.gmail.com>
Date: Wed, 21 Mar 2012 12:06:40 +0530

Dear AmberUsers,

I am doing a metalloprotein simulation. I have parameterized the metal site
using MCPB. The metal site contains a water molecule to which the metal
coordinates. When i performed MCPB, I renamed the metal as MOH and then
parameterized. Till now everything looks good. Now, when i want to
integrate the result into an MD simulation, I am following Amber Tutorial
A1. I am confused about the following:

1) when we modify the pdb file such that HIS is changes to HID or CYS is
changes to CYX, should we also modify that particular water molecule to
MOH. and then protonate the system
2) as with other residues should we give that water molecule an arbitary
name and provide the specific library file to tleap.

IN short, i want to know how such water molecule is treated considering
that the frcmod file that we generate from MCPB have taken into
consideration the water molecule coordination.

please help.

Thanks & Regards,
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Received on Wed Mar 21 2012 - 00:00:03 PDT
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