Hi AMBER,
I want to run a simulation with the special amino acid ˇ°PTRˇ±. However, the ff12SB could not recognise PTR. There are some errors.
Could you please suggest what I should do with it here?
Thanks!
Yunjie
Here is the pdb file:
ATOM 4743 N ALA A 102 69.638 110.691 69.057 1.00 98.37 N
ATOM 4744 CA ALA A 102 71.071 110.260 69.072 1.00100.00 C
ATOM 4745 C ALA A 102 71.235 108.976 69.916 1.00 99.49 C
ATOM 4746 O ALA A 102 70.414 108.725 70.803 1.00100.00 O
ATOM 4747 CB ALA A 102 71.951 111.400 69.619 1.00 97.83 C
ATOM 4748 N ALA A 103 72.255 108.163 69.589 1.00100.00 N
ATOM 4749 CA ALA A 103 72.595 106.888 70.269 1.00 99.85 C
ATOM 4750 C ALA A 103 73.436 105.979 69.340 1.00 98.84 C
ATOM 4751 O ALA A 103 72.891 105.066 68.700 1.00100.00 O
ATOM 4752 CB ALA A 103 71.324 106.141 70.719 1.00 98.64 C
ATOM 4753 N PRO A 104 74.764 106.220 69.251 1.00 97.44 N
ATOM 4754 CA PRO A 104 75.721 105.470 68.413 1.00 96.64 C
ATOM 4755 C PRO A 104 75.801 103.950 68.598 1.00 96.19 C
ATOM 4756 O PRO A 104 75.575 103.446 69.701 1.00 98.16 O
ATOM 4757 CB PRO A 104 77.063 106.114 68.769 1.00 96.00 C
ATOM 4758 CG PRO A 104 76.682 107.518 69.064 1.00 97.97 C
ATOM 4759 CD PRO A 104 75.442 107.342 69.921 1.00 95.63 C
HETATM 4760 N PTR A 105 76.115 103.238 67.507 1.00 94.55 N
HETATM 4761 CA PTR A 105 76.250 101.767 67.527 1.00 89.48 C
HETATM 4762 C PTR A 105 77.528 101.477 68.331 1.00 88.77 C
HETATM 4763 O PTR A 105 78.555 102.179 68.244 1.00 86.02 O
HETATM 4764 CB PTR A 105 76.419 101.195 66.097 1.00 86.58 C
HETATM 4765 CG PTR A 105 75.189 101.303 65.254 1.00 83.20 C
HETATM 4766 CD1 PTR A 105 73.953 100.824 65.776 1.00 81.53 C
HETATM 4767 CD2 PTR A 105 75.236 101.832 63.929 1.00 79.53 C
HETATM 4768 CE1 PTR A 105 72.767 100.869 65.010 1.00 81.88 C
HETATM 4769 CE2 PTR A 105 74.038 101.881 63.143 1.00 79.06 C
HETATM 4770 CZ PTR A 105 72.802 101.394 63.694 1.00 77.82 C
HETATM 4771 OH PTR A 105 71.588 101.410 62.956 1.00 74.75 O
HETATM 4772 P PTR A 105 71.461 102.111 61.550 1.00 71.17 P
HETATM 4773 O1P PTR A 105 72.192 103.480 61.654 1.00 72.66 O
HETATM 4774 O2P PTR A 105 72.253 101.205 60.602 1.00 69.87 O
HETATM 4775 O3P PTR A 105 70.023 102.293 61.152 1.00 69.63 O
ATOM 4776 N LEU A 106 77.444 100.397 69.108 1.00 87.31 N
ATOM 4777 CA LEU A 106 78.531 99.934 69.971 1.00 88.79 C
ATOM 4778 C LEU A 106 79.728 99.270 69.292 1.00 87.63 C
ATOM 4779 O LEU A 106 79.769 98.045 69.169 1.00 84.64 O
ATOM 4780 CB LEU A 106 77.956 99.005 71.044 1.00 94.40 C
ATOM 4781 CG LEU A 106 76.973 99.700 72.013 1.00 98.16 C
ATOM 4782 CD1 LEU A 106 75.807 98.789 72.374 1.00100.00 C
ATOM 4783 CD2 LEU A 106 77.705 100.214 73.268 1.00100.00 C
Here is the error information:
Unknown residue: PTR number: 565 type: Nonterminal
Creating new UNIT for residue: PTR sequence: 1566
One sided connection. Residue: missing connect0 atom.
Created a new atom named: N within residue: .R<PTR 1566>
Created a new atom named: CA within residue: .R<PTR 1566>
Created a new atom named: C within residue: .R<PTR 1566>
Created a new atom named: O within residue: .R<PTR 1566>
Created a new atom named: CB within residue: .R<PTR 1566>
Created a new atom named: CG within residue: .R<PTR 1566>
Created a new atom named: CD1 within residue: .R<PTR 1566>
Created a new atom named: CD2 within residue: .R<PTR 1566>
Created a new atom named: CE1 within residue: .R<PTR 1566>
Created a new atom named: CE2 within residue: .R<PTR 1566>
Created a new atom named: CZ within residue: .R<PTR 1566>
Created a new atom named: OH within residue: .R<PTR 1566>
Created a new atom named: P within residue: .R<PTR 1566>
Created a new atom named: O1P within residue: .R<PTR 1566>
Created a new atom named: O2P within residue: .R<PTR 1566>
Created a new atom named: O3P within residue: .R<PTR 1566>
One sided connection. Residue: missing connect1 atom.
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Received on Tue May 22 2012 - 20:00:04 PDT
