AMBER Archive (2008)

Subject: Re: AMBER: antechamber problem

From: Junmei Wang (junmwang_at_gmail.com)
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: ..."

Best

Junmei

On Jan 10, 2008 11:49 AM, gurpreet singh <gps.iitm_at_gmail.com> 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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