[gmx-users] About topology construction for Cyclic peptide
scvsankar_agr at yahoo.com
Mon Sep 17 03:50:59 CEST 2012
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
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?
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