[gmx-users] About pdb2gmx for cyclic pepetide

vidhya sankar scvsankar_agr at yahoo.com
Sat Sep 15 05:37:47 CEST 2012

Dear Justin  and other Gromacs users ,
                    Thank you for your previous reply
           Again i Have tried  the option -missing when i use pdb2gmx tool i have got errror as follows
My command is 

./pdb2gmx_d -f 2KDQ.pdb -o 2KDQ.gro -p 2KDQ.top  -missing -ignh -ter

There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.

 I went through a Mailing Archive Yet no body explain the proper Topology construction for cyclic peptide 

It Discussed about Manual editing of topology But in my case it is headache  

Because my cyclic peptide contains large number of atom 

How to solve this problem without manual editing

With Regards

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