Re: Re: [AMBER] how to get the hydrophobic area for a particlar region

From: Billy Miller III <>
Date: Fri, 26 Mar 2010 22:44:40 -0400

If you search the VMD archives you can find many references to the 'measure'
command for calculating sasa. There is also a tcl script (_sasa_res.tcl)
that can be found online (
that attempts to automate the process for you.

I hope this helps.

-Bill Miller

On Fri, Mar 26, 2010 at 10:26 PM, qiaoyan <> wrote:

> Dear professor:
> I try to use your method in vmd, but I don't know how to do this, while
> file should I import into vmd, when I import a pdb file into it, and "set
> protein [atomselect top "mrna25"]", there is an error "atomselect: cannot
> parse selection text: mrna25", I really don't know what to do.
> Best Regards.
> Yours sincerely,
> Yan Qiao.
> 2010-03-26
> -----------------------------------------------
> State Key Lab of Molecular Reaction Dynamics (SKLMRD),
> Dalian Institute of Chemical Physics(DICP),
> the Chinese Academy of Sciences(CAS),
> Zhongshan Road457, Dalian City,
> Liaoning Province 116023,P. R. China
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Received on Fri Mar 26 2010 - 20:00:03 PDT
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