[gmx-users] About topology construction for Cyclic peptide

vidhya sankar scvsankar_agr at yahoo.com
Mon Sep 17 03:50:59 CEST 2012

Dear Mark,
                      Thank you for your reply
I have used the peptide  FXXXXLF 

For that  pdb2gmx construct topology successfully with -ter  choosing any thing  for both terminal.

But When i Choose none with -ter for both terminal It  again shows error as follows
Fatal error:
There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.

For your Convenience i have pasted the previous discussion
That suggests you have a problem with your coordinate file that is 
independent of your attempt to cyclize. Can you generate a topology for 
FXXXXL with a) -ter choosing none, b) -ter choosing anything else?

With Regards

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