Yes, I believe you are correct that the crosslink command is unrelated to
the prep file. However, it is true that crosslink creates all
bond/angle/dihedral interactions in the parameter file. I use it all the
time to connect non-natural amino acids and synthetic polymers together.
This was very difficult to do before I found the crosslink command; now it's
easy.
On Thu, Sep 15, 2011 at 5:39 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > 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 Fri Sep 16 2011 - 09:30:04 PDT
