Hi Baljinder,
> I am working on protein with three phophorylated residues. Parameters for
> these residues was generated using ANTECHAMBER and was uploaded and it
> seemed working . But finally while uploading the protein tleap gave this
> message:
> *> apoprotein= loadpdb apoprotein.pdb
> Loading PDB file: ./apoprotein.pdb
> One sided connection. Residue: Displayed missing connect0 atom.
> One sided connection. Residue: missing connect1 atom.
> One sided connection. Residue: Displayed missing connect0 atom.
> One sided connection. Residue: missing connect1 atom.
> One sided connection. Residue: Displayed missing connect0 atom.
> One sided connection. Residue: missing connect1 atom.
> total atoms in file: 2717
> Leap added 2660 missing atoms according to residue templates:
> 2660 H / lone pairs*
> I am working on AMBER 10.
it seems that you have issues with the definition of the backbone
connection atoms within your new residues.
Maybe the parameters you need are readily available from
http://www.pharmacy.manchester.ac.uk/bryce/amber
so that you don't have to reinvent the wheel but can rely on already
published work.
Regards,
Anselm
Bioinformatik
Institut für Biochemie
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
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Received on Fri Dec 10 2010 - 07:30:02 PST
