AMBER Archive (2007)

Subject: Re: AMBER: implicit solvent simulations

From: WANG,YING (wangying_at_ufl.edu)
Date: Tue Dec 11 2007 - 22:00:59 CST

Hi,
Thanks a lot!

YW

On Tue Dec 11 22:49:57 EST 2007, liu junjun <ljjlp03_at_gmail.com>
wrote:

> 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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--
WANG,YING
Mechanical and Aerospace Engineering
University of Florida
Office: NEB 139
TEL: 001-352-846-3030

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