Hi Ying,
I agree that you should keep the waters that play important structural
roles, although this is probably only a few of the waters in the PDB file.
Most water in PDB files are on the protein surface. A word of caution,
though--I previously noticed a bug that results in incorrect radii for the
hydrogens of water. This does not matter at all for explicit solvent
calculations, but it does matter for implicit. See this thread for details
and how you can fix it. You'll have to change the solvents.lib file.
http://archive.ambermd.org/200701/0161.html
Also note that in the thread, David Case states that they haven't ever
really tried to parameterize water molecules for implicit solvation
calculations.
Steve
-----Original Message-----
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
liu junjun
Sent: Tuesday, December 11, 2007 10:50 PM
To: amber.scripps.edu
Subject: Re: AMBER: implicit solvent simulations
Hi Ying,
In general you should remove the waters when you simulate with
implicit solvation model. However, some waters in the active site play
important role in stabilizing protein. For these waters you'd better
keep them even in implicit solvation model.
Best Regards!
Junjun
On Dec 11, 2007 2:21 PM, WANG,YING <wangying.ufl.edu> wrote:
> Hi, Dear all,
> I try to perform a simulation of protein in implicit solvent
> simulation. But the pdb file has water molecules, should I delete
> it or keep it in the md process?
> Thanks a lot in advance!
>
> YW
>
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Received on Sun Dec 16 2007 - 06:07:05 PST
