On Fri, Sep 16, 2011, Sidney Elmer wrote:
> 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.
Both "bond" and "crosslink" create a bond between two atoms; they differ only
in how the atoms are identified. The crosslink command is a bit redundant,
and the Users' Manual doesn't even describe it, but you can type "help
crossLink" at the command prompt to see how to use it. The "bond" command can
also be used to make what are commonly called crosslinks; see, e.g. the
very simple example on p. 17 of the Amber11 Users' Manual.
[Note: if there is some other difference between "bond" and "crosslink", then
the above is wrong, and we should find out and document what the difference
is.]
....dac
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Received on Sat Sep 17 2011 - 06:30:03 PDT
