Re: [PyMOL] [Apbs-users] Windows/Cannot generate .dx file at APBS

[Nathan B. <ba...@cc...>]

Hi Georgios --


> I am a newcomer in this field and the use of APBS. I am trying to  
> produce
> an electrostatic potential map for a protein surface and I am using
> Windows XP. Although I have installed succesfully Pymol v0.99, APBS  
> v0.4.0
> and the M.Lerner's plug-in,following Lerner's instructions, I can  
> load my
> pdb file, I can generate the .pqr and .in files, but the programme  
> doesn't
> generate the .dx file resulting to the message:
>
> ObjectMapLoadDxFile-Error:Unable to load file!

This typically means (1) something is misconfigured in the APBS/PyMOL  
setup such as spaces in the path to the APBS binary, etc., or (2)  
something went wrong with the APBS calculation.  To rule out the  
second case, can you locate the APBS input file and PQR file you're  
using with these calculations and send them along for debugging  
purposes?

> Is there any incopatibility or lack of commands or scripts that  
> elude me?
> I tried the VMD v1.8.5 and v1.8.4 to visualize the electrostatic  
> potential
> following the instructions from the tutorial, but the procedure is  
> stopped
> at the same stage... Cannot load the .dx file because it doesn't  
> exist..

This definitely sounds like a probably with the calculation -- the  
relevant APBS input and PQR files should help us track this down.

Thanks,

Nathan


> I searched the APBS,Pymol and VMD forums but I couldn't find a  
> solution.
> Please Help me!
>
> Villias Georgios
> Bioinformatics Postgraduate student
> University of Athens - Greece
>
>
> ---------------------------------------------------------------------- 
> ---
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to  
> share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php? 
> page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> apbs-users mailing list
> apb...@li...
> https://lists.sourceforge.net/lists/listinfo/apbs-users

--
Associate Professor, Dept. of Biochemistry and Molecular Biophysics
Center for Computational Biology, Washington University in St. Louis
Web: http://cholla.wustl.edu/