AMBER Archive (2008)

Subject: Re: AMBER: antechamber problem

From: gurpreet singh (gps.iitm_at_gmail.com)
Date: Thu Jan 10 2008 - 22:05:38 CST

Thanks for your reply Junmei

In that case than what is the reason for the absence of all Oxygen atoms
from the output NEW.PDB and prepi files. Any idea?

Regards
Gurpreet

On Jan 10, 2008 11:59 PM, Junmei Wang <junmwang_at_gmail.com> wrote:

> 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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