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

From: Balazs Jojart <>
Date: Sat, 27 Mar 2010 13:28:13 +0100

Hi Yan,
I suppose that "mrna25" stands for the name of your protein.
You have to use the *protein* instead of it, because this is the keyword
in vmd for all protein atoms, so use the following:
set protein [atomselect top "protein"]
Hope this helps.

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 Sat Mar 27 2010 - 05:30:02 PDT
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