Hello –

 

You can visualize the potential on the solvent-excluded surface in PyMOL; it’s one of the options on the APBS-TOOLS menu.  You can also use this surface to define the dielectric coefficient in your APBS calculation by using the “srfm mol” command in your APBS input file.

 

I hope this helps,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

 

From: Heng Yang [mailto:daisyang095@gmail.com]
Sent: Saturday, October 15, 2011 11:58 AM
To: apbs-users@googlegroups.com
Cc: apbs-users@lists.sourceforge.net
Subject: Re: [apbs-users] Can APBS describe the surface using Solvent Excluded Surface instead of Solvent Accessible Surface ?

 

Sorry for the confusing word.
my project is to calculate the electrostatic potential on the protein surface, when I use APBS in pymol, I can see the electrostatic potential mapped on the solvent-accessible surface , and I can also save the surface points with  its corresponding electrostatic value to a file.
Right now , i am thinking of generating the electrostatic potential on the solvent excluded surface (molecular surface) instead of solvent accessible surface.
so my question is can I use APBS to calculate the electrostatic potential of each points on the solvent excluded surface in pymol or VMD ?
Thanks

On Sat, Oct 15, 2011 at 2:10 PM, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:

Can you please say a bit more about what you mean by “gives”?  Are you referring to the surface used in the calculation or the solvent-accessibility maps written as output?

 

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://kdi.pnl.gov/bios/baker.stm

 

From: Daisyang [mailto:daisyang095@gmail.com]
Sent: Thursday, October 13, 2011 11:25 AM
To: apbs-users@googlegroups.com
Subject: [apbs-users] Can APBS describe the surface using Solvent Excluded Surface instead of Solvent Accessible Surface ?

 

 

When I run APBS , it gives me the Solvent Accessible Surface, but I prefer the Solvent Excluded Surface,is there any way to change it to Solvent Excluded Surface?

Thanks

Daisy 


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Daisy