AMBER Archive (2008)

Subject: AMBER: antechamber problem

From: gurpreet singh (
Date: Thu Jan 10 2008 - 11:49:15 CST

Hi Amber Users

I am using Antechamber module of Amber 9.0 for preparing the prepi file for
my compound.
I gave the following command

antechamber -i ionic.log -fi gout -o ionic.prep -fo prepi

while execution I got the following error:

 "Bond types are assigned for valence state 13 with penalty of 2"

What is the reason for this error?

As a result, I am although getting the prepi file but some of the oxygen
atoms were not coming in the resultant prepi and NEW.PDB files generated
by antechamber.

Please explain me the reason for this unusual behaviour.

I am having a Nitrate anion and another cation in my input system and the
oxygens of Nitrate are not coming.

THanks & Regards

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to