> 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.
If the bond cmd does not do this too, then there is a bug.
Bill
> 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 - 15:30:02 PDT
