Re: [AMBER] Water coordinated with transition metal

From: ashwini gupta <>
Date: Wed, 21 Mar 2012 16:03:29 +0530

Dear Ben,

Yes it is. :)

So, while preparing the prmtop and inpcrd file I essentially fix the water
molecule that coordinates with metal by naming it as MOH while the other
water molecules are name ad HOH. Is this correct. shouldn't the water
molecules move ard and different water molecules interact with the metal at
different time points. Will the two things mean the same??


On Wed, Mar 21, 2012 at 3:10 PM, Ben Roberts <> wrote:

> Hi Ashwini,
> On 21/03/2012, at 10:09 PM, ashwini gupta wrote:
> > However, when i prepare the prmtop file and inpcrd file for further MD
> > simulation, should i name that particular water molecule as MOH or
> should i
> > let leap solvate the system.
> Is it not named as MOH already in the PDB file produced by MCPB?
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Received on Wed Mar 21 2012 - 04:00:02 PDT
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