One thing you need to pay attend is the radii in VMD or PyMol are
different from those in Amber ... if you want consistency between your
mmpbsa analysis and whatever analysis you have in mind, you may need to
use the same parameters for both calculations.
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/
==========================================
Balazs Jojart wrote:
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
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>
>
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Received on Thu Mar 25 2010 - 12:00:02 PDT
