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

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 26 Mar 2010 19:42:04 -0700

On Fri, Mar 26, 2010 at 7:26 PM, qiaoyan <qiaoyan.dicp.ac.cn> 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.
>

"mrna25" should be something some type of selection that vmd
understands. For instance "all" for the entire protein. "all not
water" for the whole system without waters, "resid 1 to 25" for the
first 25 residues, etc.

Good luck!
Jason

>  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
>  E-mail: qiaoyan.dicp.ac.cn
>  Office Phone: +86+411+84379352
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 26 2010 - 20:00:02 PDT
Custom Search