[gmx-users] struggles with cyclic peptides

Nikhil scinikhil at gmail.com
Sun Sep 13 19:45:49 CEST 2015

Thank you very much Justine,
now it making bond between first and last residue of amino acids but there 
as an extra oxygen atom is coming  when i select any option other than 
None.but when i select None for the second terminals it shows an error 
There is a dangling bond at at least one of the terminal ends. Fix 
yourcoordinate file, add a new terminal database entry (.tdb), or select 
 proper existing terminal entry.**For more information and tips for 
troubleshooting, please check the GROMACS*

should i edit the .tdb file ?
thanks in advance

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