AMBER Archive (2007)

Subject: Re: AMBER: implicit solvent simulations

From: liu junjun (ljjlp03_at_gmail.com)
Date: Tue Dec 11 2007 - 21:49:57 CST

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_at_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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