antechamber and its prepin files

From: Steve Seibold <>
Date: Wed, 19 Feb 2003 14:11:23 -0500

I hope someone can assist me.
I am constructing ligands to use in AMBER. My problem is that when I build
a simple molecule (carbon, hydrogen and oxygen) using some program (e.g.
MOE) that will output a pdb file ANTECHAMBER is not able to convert it into
a correct prepin file. I have tried, successfully a few times, to rename the
carbon atoms from C to CA etc. Most of the time it takes hours (to days) for
me to locate something that will make a correct prepin file to load into
xleap. I keep getting carbon atoms and hydrogens referred to as DU in my
prepin files (along with nan0x7ffffffff). Is there some logical format that
I can use to convert my pdb files to a prepin file without this trouble? I
would appreciate any help in this area.

Thanks, Steve
Received on Wed Feb 19 2003 - 19:53:01 PST
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