AMBER Archive (2008)

Subject: AMBER: Atom names CL and four characters

From: Francesco Pietra (
Date: Fri Oct 24 2008 - 13:55:05 CDT


1st Question: prepin/frcmod (for an organic compound containing
covalent chlorine), coming from Antechamber in AmberTools1.2 are not
accepted by leap:

Atom .R<AA1 ###>.A<CL ##> does not have a type.

I guess that leap expects "Cl" for chlorine.How to arrange so that
Antechamber prepares files accordingly?

2nd Related Question: As the protein for the above complex (coming
from work up with Chimera) has atom names with four
characters/numbers, are, for example,


accepted by Amber10/AmberTools1.2, or should they be edited to


as it was the case with Amber9?

francesco pietra
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