[gmx-users] About topology construction for yclic pepetide

Mark Abraham Mark.Abraham at anu.edu.au
Mon Sep 17 02:59:32 CEST 2012

On 17/09/2012 2:55 AM, vidhya sankar wrote:
> Dear Mark ,
>                         Again    Thanks  for you reply
> After Editing my pdb  file from intial FXXXXL to FXXXXLF format
> Then i Run pdb2gmx for my linaer    pdb  file , i have selected none for both termini ( with -ter option) as you mailed me in the previous mail
> I have got error as follows
> Fatal error:
> There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.
> How to Rectify this error

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?


> For  your  Remembrance i pasted your previous Discussion
> 1) Take your initial coordinate file, make a copy and in it make a copy
> of the first residue and place it after the last residue, taking care to
> obey the format of the file you're using, and update things like atom
> counts and atom and residue indices. The coordinates of the copied atoms
> don't matter. Now you have a coordinate file for FXXXXLF.
>   2) Process that with pdb2gmx using -ter and choosing "none". This has
> built a linear topology for FXXXXLF, with a correct L-to-F link for you
> to use as a template for making a cyclic FXXXXL.
> Thanks in Advance

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