From: Hélder Bandarra Tavares (
Date: Mon Jun 01 2020 - 08:31:51 CDT

Hello Josh,

It ended up working, I don't know exactly what I changed. But thanks for the help anyway.


From: Josh Vermaas <>
Sent: 27 May 2020 17:49:31
To: Hélder Bandarra Tavares
Subject: Re: vmd-l: Extrabonds issue

Is there a newline at the end of the file? NAMD's parser is picky, and wants an empty line at the end of files it reads in.


On Wed, May 27, 2020 at 4:51 AM Hélder Bandarra Tavares <<>> wrote:

I'm trying to use Extrabonds to keep 2 atoms close to each other, so I created a .exb file containing "bond 7 86 1 5" and wrote in the configuration file "

extraBonds on
extraBondsFile Extrabonds.exb". However, when I try to run it I get the following message:

Charm++ fatal error:
FATAL ERROR: ABNORMAL EOF FOUND - buffer=*bond 7 86 1 5*"

Where 7 and 86 are the atoms I want to keep at a distance of 5 A. Do you know what I'm doing wrong?

Thank you in advance,
Hélder Tavares