[AMBER] error in reading protein file

From: Arunima Shilpi <writetoash28.gmail.com>
Date: Tue, 8 Apr 2014 11:28:18 +0530

Dear Sir


Presently I am studying protein-ligand interaction in which one of the
residue along the active site have been mutated to ILE . Now when I load
the protein in tleap it shows the following error

complex=loadpdb C1191I_ZINC7271_min.pdb
Loading PDB file: ./C1191I_ZINC7271_min.pdb
Created a new atom named: CD within residue: .R<ILE 709>
  Added missing heavy atom: .R<ILE 709>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 731>
  Added missing heavy atom: .R<ILE 731>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 752>
  Added missing heavy atom: .R<ILE 752>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 766>
  Added missing heavy atom: .R<ILE 766>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 828>
  Added missing heavy atom: .R<ILE 828>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 835>
  Added missing heavy atom: .R<ILE 835>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 899>
  Added missing heavy atom: .R<ILE 899>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 923>
  Added missing heavy atom: .R<ILE 923>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 942>
  Added missing heavy atom: .R<ILE 942>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 974>
  Added missing heavy atom: .R<ILE 974>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 977>
  Added missing heavy atom: .R<ILE 977>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 980>
  Added missing heavy atom: .R<ILE 980>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 995>
  Added missing heavy atom: .R<ILE 995>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 997>
  Added missing heavy atom: .R<ILE 997>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1020>
  Added missing heavy atom: .R<ILE 1020>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1114>
  Added missing heavy atom: .R<ILE 1114>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1121>
  Added missing heavy atom: .R<ILE 1121>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1145>
  Added missing heavy atom: .R<ILE 1145>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1147>
  Added missing heavy atom: .R<ILE 1147>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1268>
  Added missing heavy atom: .R<ILE 1268>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1269>
  Added missing heavy atom: .R<ILE 1269>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1308>
  Added missing heavy atom: .R<ILE 1308>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1319>
  Added missing heavy atom: .R<ILE 1319>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1340>
  Added missing heavy atom: .R<ILE 1340>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1362>
  Added missing heavy atom: .R<ILE 1362>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1367>
  Added missing heavy atom: .R<ILE 1367>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1382>
  Added missing heavy atom: .R<ILE 1382>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1396>
  Added missing heavy atom: .R<ILE 1396>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1446>
  Added missing heavy atom: .R<ILE 1446>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1519>
  Added missing heavy atom: .R<ILE 1519>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1538>
  Added missing heavy atom: .R<ILE 1538>.A<CD1 14>
Created a new atom named: CD within residue: .R<ILE 1542>
  Added missing heavy atom: .R<ILE 1542>.A<CD1 14>
  Added missing heavy atom: .R<CALA 1550>.A<OXT 11>
  total atoms in file: 7224
  Leap added 7130 missing atoms according to residue templates:
       33 Heavy
       7097 H / lone pairs
  The file contained 32 atoms not in residue templates

I request you to kindly guide me rectifying the above error.

Regards

Arunima
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Received on Mon Apr 07 2014 - 23:00:03 PDT
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