Hi Michael -

I think there may be two different issues here - the deprecated warnings are definitely due to an older version of PyMOL and/or the plugin, but even with the new version of each I duplicate the

ObjectMapLoadDXFile-Error: Unable to open file!

that others are apparently seeing. Any thoughts?

Thanks!

Todd

On 2/7/06, Michael George Lerner < mlerner@umich.edu> wrote:

Hi,

Please download and install the most recent version of the PyMOL/APBS
Plugin from my webpage (http://www-personal.umich.edu/~mlerner/PyMOL/).
The version you're using doesn't work with the current version of APBS.
Also, I'm not sure if PyMOL can automatically generate parameters for RNA.
If it can't, you might want to use pdb2pqr.

-michael

--
www.umich.edu/~mlerner |                        _  |Michael Lerner
This isn't a democracy;| ASCII ribbon campaign ( ) |   Michigan
it's a cheer-ocracy.   |  - against HTML email  X  |  Biophysics
-Torrence,  Bring It On|                       / \ | mlerner@umich

On Tue, 7 Feb 2006, Blanton Tolbert wrote:

> Hi
>
> I am trying to use apbs to calculate the electrostatic surface of an rna
> molecule.  I get the following error message:
>
> Parsing input file pymol-generated.in...
> parsePBE:  Warning -- parsed deprecated "bcfl 1" statement
> parsePBE:  Please use "bcfl sdh" instead.
> NOsh:  Warning -- parsed deprecated statment "chgm 1".
> NOsh:  Please use "chgm spl2" instead!
> parsePBE:  Warning -- parsed deprecated "srfm 1" statement.
> parsePBE:  Please use "srfm smol" instead.
> parsePBE:  Warning -- parsed deprecated "calcenergy 0" statement.
> parsePBE:  Please use "calcenergy no" instead.
> parsePBE:  Warning -- parsed deprecated "calcforce 0" statement.
> parsePBE:  Please use "calcforce no" instead.
> PBEparm_check: SDENS not set!
> NOsh:  MG parameters not set correctly!
> Error while parsing input file.
> ObjectMapLoadDXFile-Error: Unable to open file!
>
> could some one please provide me some insight into how i can correct this
> problem.
>
> thanks,
>
>
>
> Blanton Tolbert
> Graduate Student
> University of Rochester
> Biophysics and Structural Biology
> 585-275-5189
> blanton_tolbert@urmc.rochester.edu
>
>
>
>
>
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