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

From: Balazs Jojart <>
Date: Thu, 25 Mar 2010 19:14:33 +0100

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,

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: Phones: (949) 824-9528, 9562
> Web:
> ==========================================
> 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:
>> Office Phone: +86+411+84379352
>> _______________________________________________
>> AMBER mailing list
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Received on Thu Mar 25 2010 - 11:30:05 PDT
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