AMBER Archive (2008)

Subject: AMBER: (no subject)

From: Daniel B. Kaplan (dkaplan_at_stevens.edu)
Date: Sun Jun 22 2008 - 18:46:17 CDT

I have a chain of benzene rings in a .pdb file. I want to put an atom
below the chain to simulate a probe. In the .pdb file everything works
fine; however, when I run the file through antechamber to convert it to
a .prepin file, the output contains no information about the atom I
placed in the .pdb file except three coordinates (two of which are nan
"not a number"). Also, it contains conflicting an X in the column which
describes how many atoms that atom is connected to. How do I resolve
this issue.
Dan
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