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

From: Ray Luo <>
Date: Thu, 25 Mar 2010 09:49:27 -0700

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 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

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 - 10:00:02 PDT
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