[gmx-users] About topology construction for yclic pepetide

vidhya sankar scvsankar_agr at yahoo.com
Sun Sep 16 18:55:50 CEST 2012

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

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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