Re: [AMBER] Water coordinated with transition metal

From: Ben Roberts <>
Date: Wed, 21 Mar 2012 20:21:35 +1300

Hi Ashwini,

On 21/03/2012, at 7:36 PM, ashwini gupta wrote:

> 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.

Do you mean that you renamed the metal ion as MOH, or its attached hydroxide? Conventionally, the name MOH is used for hydroxide ions, bound to metals as it might be.

> 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 the past, I've usually given metal-bound water molecules for MCPB a new name, at the time of going through the MCPB process. It creates a little more clutter in the form of additional residue templates, but the output is easier to interpret and if you do that you'll know you won't be overridden by a default parameter set.

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Received on Wed Mar 21 2012 - 00:30:03 PDT
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