[gmx-users] About topology construction for Cyclic peptide

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 17 09:07:36 CEST 2012

On 17/09/2012 11:50 AM, vidhya sankar wrote:
> 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.

OK, well you can work with that topology as your template for the same 
kind of procedure, but you will have to pay attention to the atom types 
of the N terminus of F (both N and its hydrogen atoms). They should 
match those of the N terminus of the C-terminal N in FXXXLF.

> 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.

Shrug. You're not giving your pdb2gmx commands, any useful diagnostic 
output before the error message, or any information about the terminal 
residues, so you're making your own life hard by making every one's hard.


> 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
> S.vidhyasankar

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