Hi Ben,
Thanks for the quick reply.
Sorry if u misunderstood. I have renamed the hydroxide attached to the
metal as MOH (as also explained in the MCPB tutorial). It makes it easier
to interpret as also suggested by you. I have successfully completed this
part of the calculation.
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.
Thanks & Regards
Ashwini
On Wed, Mar 21, 2012 at 12:51 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> 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.
>
> Ben
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Received on Wed Mar 21 2012 - 02:30:02 PDT
