From: Christopher Neale (
Date: Thu Jul 26 2012 - 21:03:35 CDT

Dear users:

this took me a while to figure out so I am posting it for posterity. This is VMD 1.9.1 with Windows 7.

When you use the menu to load a file into VMD, the file gets a simple filename (e.g. name.pqr). However, when you drag and drop the .pqr file into the main VMD screen, the file gets a name that has the full directory (e.g. C:\Users\Chris\Desktop\em_oneprot.pqr). When one then runs APBS, the program attempts to load C:/working_directory/apbs.#{C:/Users/Chris/Desktop/em_oneprot.pqr where the curly bracket certainly looks strange. If one then renames the molecule that was dragged and dropped to load into VMD so that its name no longer has the directory structure, then APBS works fine.

A fix would be nice, but the renaming workaround is fine too. I would appreciate it if this could work its way into the documentation of the APBS plugin online, if possible, so that others don't have to troubleshoot this.

Thank you,