AMBER Archive (2008)

Subject: Re: AMBER: antechamber problem

From: Junmei Wang (
Date: Thu Jan 10 2008 - 12:29:23 CST

This is not an error, it is just for information purpose. In antechamber,
all this kinds of message starting with "Info: ...". For error message, it
comes with "Error: ..."



On Jan 10, 2008 11:49 AM, gurpreet singh <> wrote:

> 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
> Gurpreet

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