Re: Abnormal EOF Error in Extra Bonds File

From: Jim Phillips (
Date: Tue May 10 2011 - 20:15:18 CDT

You're probably missing a carriage return at the end of the file and the
readline function is confused that the file ended before the line did.
You can see the missing newline if you cat the file and vi will say
"Incomplete last line" when you edit it.


On Tue, 26 Apr 2011, Eli Fine wrote:

> Hello,
> I'm trying to add a single extra bond to my NAMD simulation.
> I can run the NAMD file fine if I comment out the two extra bond lines
> #extraBonds yes
> #extraBondsFile azoTrans.txt
> but when I run it with those enabled, then it gives me this error
> FATAL ERROR: ABNORMAL EOF FOUND - buffer=*bond 8509 8644 50. 17.*
> my extrabonds file consists of just these two lines:
> #atom IDs are 0-indexed
> bond 8509 8644 50. 17.
> I have tried running it without the decimal points in the extra bond file
> and with 0s after the decimal points, but nothing seems to work.
> As far as I can tell I am following the instructions posted online, but
> there are no example files and no one else seems to be running in to this
> problem, so I'm confused.
> Thanks,
> Eli

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