On Mon, Nov 7, 2011 at 7:52 AM, James Starlight <jmsstarlight.gmail.com>wrote:
> Another my question about XLEAP relate to the build-up missing residues in
> my initial structure (e.g my iniial structure is the X-ray with the missing
> residues)
>
> As I've understood during loading of my pdb AmberTools always build missing
> atoms like H-atoms. But could I also build missing residues ( e.g I could
> obrtain list of such reidues in the hader of my pdb or manually)?
>
As far as I know, you need to have at least one atom from your missing
residue in your PDB sequence. It will fill in all missing ones from a
template, but won't do that unless it knows that residue is there. It will
definitely add heavy atoms in addition to hydrogens if they're missing,
though.
I don't think leap reads the header sections of the PDB, but I may be wrong
here.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Nov 07 2011 - 06:00:05 PST
