AMBER Archive (2006)

Subject: Re: AMBER: How could I simulate lipid membrane with AMBER9.0?

From: 曹冉 (tomcao_at_mail.bnu.edu.cn)
Date: Thu Dec 07 2006 - 19:46:44 CST

Yes.Of course,if you want to simulate the full property.
By the way,if you make sure adding membrane into your simulation system,do you
know how to deal with the lipid membrane with amber9?

Good luck and best wishes!
Ran Cao

在您的来信中曾经提到:
>From: Fenghui Fan <fenghui_fan_at_yahoo.com>
>Reply-To: amber_at_scripps.edu
>To: amber_at_scripps.edu
>Subject: Re: AMBER: How could I simulate lipid membrane with AMBER9.0?
>Date:Wed, 6 Dec 2006 18:49:09 -0800 (PST)
>
>One simple queastions, if the membrane protein
> contains both the hydrophobic part and the hydropholic
> part, shoud we make a box containg both water and the
> lipid bilayer?
>
> Best regards.
>
> Fenghui Fan
>
>
> --- 曹冉 <tomcao_at_mail.bnu.edu.cn> wrote:
>
> > Hi all
> >
> > I want to perform MD simulation on membrane protein
> > in lipid bilayer
> > environment,but how could I set the force field
> > parameters for lipid such as DPPC
> > membrane?I've found several papers related to
> > simulation of lipid membrane using
> > AMBER4.0(with OPLS as force field parameter for
> > lipid membrane),but I've no idea
> > about how to set this in my current issue:AMBER9.0.
> >
> > Thanks a lot!
> > Ran Cao
> >
> >
> >
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>
>
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