AMBER can give you a per atom solvent accessible surface area by using
sander to perform a PB calculation. You can set imin=5 to post-process your
simulated trajectory. See the AMBEr manual for specifics on setting the
probe radius and other variables. However, if you are looking to calculate
the SASA for the entire system I would suggest using the 'measure sasa'
command in VMD. This will allow you to specify a particular part of your
system for analysis, or it can be performed on the entire system. Check the
VMD list and manual for more specifics on how to use this command. In
particular, I know there is a tcl script available online (
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-8424/_sasa_res.tcl)
that can be sourced within VMD that will perform this calculation.
Good luck!
-Bill
On Wed, Apr 21, 2010 at 11:27 PM, Yunfen Wang <wangfen041237.163.com> wrote:
> Hi all,
> I mean to caculate solvent accessible surface for my systerm of Pr with
> solvent . I like to use solvent molecule as probe sphere ,and Pr as object.
> How can I do that ?
> Thanks a lot , all.
> wang
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Apr 21 2010 - 21:00:02 PDT
