AMBER Archive (2009)

Subject: [AMBER] test charge

From: Dan Kaps (dan.kaps_at_yahoo.com)
Date: Wed Feb 18 2009 - 20:27:32 CST

Amber List:
Hi I am investigating the effects of a test charge (in this case simply a hydrogen atom) on a long chain of benzene rings. The test charge is placed directly above the center benzene ring. I am attempting to run the .pdb file through antechamber to get the .prepin file; however, I am having some difficulties. The .prepin file replaces the test charge with an "X." It literally just says "X" instead of H. Also, it replaces two of the spacial coordinates with "nan" not a number. Does anyone know what the problem is and how I can fix it?
Much Appreciated,
Dan

      
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