From: Michael G. L. <ml...@um...> - 2006-02-07 18:33:59
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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 > bla...@ur... > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > |