Hi Yan,
in vmd you can do this with the measure sasa command.
After you load the file into vmd, open the tk console, and use the
following commands
set protein [atomselect top "protein"]
set phob [atomselect top "hydrophobic"]
set phil [atomselect top "not hydrophobic"]
measure sasa 1.4 $protein -restrict $phob
measure sasa 1.4 $protein -restrict $phil
the first value should be the hydrophobic SASA, and the second one the
hydrophilic SASA.
if you would like to calculate only the protein sasa then:
measure sasa 1.4 $protein
hope this helps,
Balazs
Ray Luo wrote:
> Usually, a surface program only prints out the total SASA. To get what
> you want, most likely you need to write your own script.
>
> One way to go is this ... if you know how to run SANDER or PBSA
> manually, you may set npbverb=1 and this will cause a printout of
> every atom's SASA. If you know which atom is hydrophobic and which
> atom is hydrophilic, they you just need to sum up relevant atomic SASAs.
>
> All the best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor in Computational
> Biochemistry and Molecular Biophysics
> Dept of Molecular Biology and Biochemistry Dept of Biomedical Engineering
> University of California, Irvine, CA 92697-3900
> Email: rluo.uci.edu Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/rayl/
> ==========================================
>
>
>
> qiaoyan wrote:
>> Hello everyone:
>> I have calculated surface area using mmpbsa, but I want to
>> obtain the hydrophobic area and hydrophilic area, how can I do this?
>> Moreover, how to get the hydrophobic area for a particlar region?
>> Thanks very much! Have a good day!
>>
>> Best Regards.
>>
>> Yours sincerely, Yan Qiao. 2010-03-25
>> -----------------------------------------------
>> 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
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Received on Thu Mar 25 2010 - 11:30:05 PDT
