AMBER Archive (2008)

Subject: AMBER: question about antechamber

From: Lynn (
Date: Thu Jan 03 2008 - 08:32:56 CST

dear all:
I am doing the job about the interaction of dioxin and protein. but when i
use antechamber to deal with 2,3,7,8-tcdd, the input format is pdb, and the
output format is prepi, it cause problem. I read the output file, it defined
carbon on the benzene ring as "ce" or "cc", not "ca"(as described in
$AMBERHOME/dat/antechamber/ATOMTYPE_GFF.DEF). And such condition caused
problem when i load frcmod file to leap, and coming-up procedure with
protein-tcdd complex. Then i use saved prmtop and inpcrd file to run
minimise and equilibrate, I found that the tcdd in complex would distort and
it cannot keep as a planar construction.

can any one help me?
Or, is there any anther way to treat protein-ligand 's pdb file , make it
analyzed correctly by leap, and do following MD simulation?


Both tcdd.pdb and tcdd.prepin are attached.

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