AMBER Archive (2008)

Subject: AMBER: Antechamber Question

From: Daniel B. Kaplan (
Date: Mon Jun 23 2008 - 11:51:28 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.
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