> Depending on your end goal, you might also want to use the "crosslink"
> command rather than "bond". "Bond" only makes a single bonding interaction
> between the two specified atoms, whereas "crosslink" makes the bond, all
> angles, and all dihedral angles according to the rules listed in your .prep
> file.
Note that these 'rules' are a template for adding missing atoms, and
are not related to the fact that there will be force field terms for
each bond/angle/dihedral involved in either case.
Beyond that, I'm not sure how crosslink could take prep structure into
account when making the bond, or why this would be desirable. There
would have to be a dummy atom on each residue that the crosslink replaces
(in order to template the position of the atom in the other residue)
and it would have to apply the rules to both residues without regard to
other atoms, resolving conflicts between the residues in an arbitrary
way, leading to a distorted structure.
I think the crosslink command may depend on having a 'connect2' atom
in the template for each residue (i.e. an atom designated for side-linking
across the chain). I'm not sure that it adds any actual value over the
bond cmd.
Bill
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Received on Thu Sep 15 2011 - 18:00:02 PDT
