[gmx-users] Bonds between New residues and Terminals

[Steven Neumann]

Dear Gmx Users,

My surface is made of 4 types of residues created on my own. They are
placed within they vdwradii away from each other. I want to keep the
surface rigid and allow it to move into only one direction (freezgrps,
freezdim). Each residue is made of one atom. The best option would be to
create bonds between or apply distnce restraints e.g. using cutoff of 1nm.

How can I create bonds between them? Shall I specify in my aminoacids.rtp
the possibilities of each of them to create bonds with any 3 others? Then
to add proper lines to specbond.dat?
I want two of them to create extra bond with my protein terminals. How to
do this using bonds? Or would you suggest distance restraints?

Thank you in advance,

Steven
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