On Tue, May 26, 2015, Chris wrote:
>
> As I say, I want prepare parameters for protein and a monosaccharide
> (non-bounded) in a crystal PDB structure, not a sugar alone.
This sounds like a distinction without a difference: if the sugar is not
covalently bonded to the protein, then one prepares amber library files and
pdb files in exactly the same way, whether or not a protein is present.
Make sure there is a TER card in your pdb file between the protein parts and
the sugar parts.
> Question comes: Such handling is OK and reasonable???( Personally, I
> think it is OK, I have checked the structure after this)
What you have described sounds OK to me. Of course, check things yourself:
e.g. run a minimization of the complex, visualize the resulting structure in
some program like VMD or Chimera, and make sure it looks like what you think
it should.
....dac
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Received on Tue May 26 2015 - 05:00:02 PDT
