[gmx-users] Creating topology with bonds over pbc

Wojciech Müller wmueller at anoa.icp.uni-stuttgart.de
Tue Oct 4 09:25:06 CEST 2011

Hi all,
Let's say I created a pdb of a B-DNA Double-Helix with amber tools. Now 
I would like to have a topology in which the last residues are bonded to 
the first. How can I do that expect of actually mess together a topology 
file by self written scripts and/or handwork? Also if create helix 
strings without substituting the terminal phosphate pdb2gmx doesn't seem 
to accept it.
Thanks for any hints,

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