AMBER Archive (2009)

Subject: [AMBER] antechamber : missed atoms

From: Khaled Barakat (
Date: Mon Jan 26 2009 - 12:54:07 CST


I am trying to use Antechamber from Ambertools 1.2 to get parameters for a set of ligands. The
input pdb files for antechamber seem to be OK . Attached is an example of these ligands along with
the NEWPDB.PDB generated by Antechamber. As you can see there are some missing atoms in the

I am using the command:
antechamber -i ref.pdb -fi pdb -o ref.prepin -fo prepi -rn UNK -s 2 -at gaff

and of course when I run the command
parmchk -i ref.prepin -f prepi -o ref.frcmod

I get Bus error.

I am wondering if some one can help me to solve this problem and preserve these atoms?

with my best regards


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