On Sat, Jan 28, 2012, James Starlight wrote:
>
> As I've wrote I've loaded my pdb in the Xleap but I cant find SEQUENCE
> SEARCH in EDITING mode of the xleap ( the protein too large so its very
> difficult to find my motif visualy).
It's certainly true that moving visually around a big protein is
difficult in xleap. But even if you could do it, just drawing in a
bond there wouldn't do you any good: to run subsequent minimization or
MD simulations, you need to create a force field for your non-standard
fragment. Francois' email gave a detailed overview of what you would have
to do. Once you have that done, and have a modified protein PDB file to
go along with it, there won't be any need to find the section in xleap:
just loading the fragment library and the pdb together will automatically
create the bond you need.
....hope this helps...dac
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Received on Sat Jan 28 2012 - 07:00:03 PST
