Re: [apbs-users] APBS output files

[Baker, N. <Nat...@pn...>]

Hello -

The multivalue tool assigns potential value to any point within the solution domain by spline interpolation.  However, it does not associate points with atoms.  The coordinate information in the output.dx file in implicitly presented in the header of that file.

The multivalue program can be called from the command line.

Good luck!
__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://nabaker.me

From: Heng Yang [mailto:dai...@gm...]
Sent: Sunday, January 01, 2012 4:32 PM
To: Baker, Nathan
Subject: Re: [apbs-users] APBS output files

HI.Nathan,

Thanks for the answer, that's very helpful, I have been struggling for this for a long time, now I have two minor questions for multivalue tool.
1, for the multivalue tool, I need to apply surface points from MSMS and the potential file, for example ,the output.dx file from APBS.
But I wonder how multivalue tool assigns potential on the surface point based on output.dx from APBS ? according to the rule of which atom is closet to the surface point? but in output.dx file ,I haven't seen the coordinates information.How does multivalue assigns potential
values onto surface points based on output.dx calculated by APBS.

2. I checked out the multivalue tool online,there is not many information, do i need any other file to compile multivalue code? or I could
simply call it via command line ?
Thank you very much and
Happy New Year

On Sat, Dec 24, 2011 at 2:07 PM, Baker, Nathan <Nat...@pn...<mailto:Nat...@pn...>> wrote:
Hello --

APBS doesn't currently provide an output of the various surface points; however, you could use a program like MSMS to accomplish this.  Once you have the surface points, you can use the "multivalue" tool from APBS to evaluate the potential at each point.

Good luck,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997<tel:509-375-3997>
http://nabaker.me


-----Original Message-----
From: Daisyang [mailto:dai...@gm...<mailto:dai...@gm...>]
Sent: Thursday, December 22, 2011 11:00 AM
To: apb...@li...<mailto:apb...@li...>
Subject: [apbs-users] APBS output files

Hi, I am using APBS command lines to generate the electrostatic surface,but the output file .dx only describes the potentials of  the grid points, But what I would like to have is a file containing the coordinates of connolly molecular surface points and its corresponding electrostatic potential,could anybody give me some hints of how to do it ?
Thanks

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