Dear Amber users, There are two phosphorylated residues in my protein, TPO183 (phosphorylated threonine) and PTR185 (phosphorylated tyrosine).I have modified the two residues in the pdb file as follows: the residue name of the atoms belong to the THR183 and TYR185 were modified back to THR and TYR respectively; the residue name of the two phosphate groups were deleted and the residue number of them were modified to 359 and 360 (the last residue number in my protein was 358, so I add two residue number for them).Though the parameters of the phosphate group atoms were included in the amber9/dat/leap/parm/parm99.dat, the 8 phosphate group atoms were not recognized by leap. so, What I want to know is that how can I deal with the two phosphorylated residues. Thanks very much!Yaxue Zhao Source pdb fileHETATM 1434 N TPO 183 HETATM 1435 CA TPO 183
HETATM 1436 CB TPO 183
HETATM 1437 CG2 TPO 183
HETATM 1438 OG1 TPO 183
HETATM 1439 P TPO 183
HETATM 1440 O1P TPO 183
HETATM 1441 O2P TPO 183
HETATM 1442 O3P TPO 183
HETATM 1443 C TPO 183
HETATM 1444 O TPO 183
HETATM 1454 N PTR 185
HETATM 1455 CA PTR 185
HETATM 1456 C PTR 185
HETATM 1457 O PTR 185
HETATM 1458 CB PTR 185
HETATM 1459 CG PTR 185
HETATM 1460 CD1 PTR 185
HETATM 1461 CD2 PTR 185
HETATM 1462 CE1 PTR 185
HETATM 1463 CE2 PTR 185
HETATM 1464 CZ PTR 185
HETATM 1465 OH PTR 185
HETATM 1466 P PTR 185
HETATM 1467 O1P PTR 185
HETATM 1468 O2P PTR 185
HETATM 1469 O3P PTR 185 Modified pdb fileATOM 1434 N THR 183
ATOM 1435 CA THR 183
ATOM 1436 C THR 183
ATOM 1437 O THR 183
ATOM 1438 CB THR 183
ATOM 1439 OG1 THR 183
ATOM 1440 CG2 THR 183
ATOM 1450 N TYR 185
ATOM 1451 CA TYR 185
ATOM 1452 C TYR 185
ATOM 1453 O TYR 185
ATOM 1454 CB TYR 185
ATOM 1455 CG TYR 185
ATOM 1456 CD1 TYR 185
ATOM 1457 CD2 TYR 185
ATOM 1458 CE1 TYR 185
ATOM 1459 CE2 TYR 185
ATOM 1460 CZ TYR 185
ATOM 1461 OH TYR 185 ATOM 3000 P 359
ATOM 3001 O1P 359
ATOM 3002 O2P 359
ATOM 3003 O3P 359
ATOM 3004 P 360
ATOM 3005 O1P 360
ATOM 3006 O2P 360
ATOM 3007 O3P 360 Problems met in leap:Creating new UNIT for residue: sequence: 366
Created a new atom named: P within residue: .R< 366>
Created a new atom named: O1P within residue: .R< 366>
Created a new atom named: O2P within residue: .R< 366>
Created a new atom named: O3P within residue: .R< 366>
Creating new UNIT for residue: sequence: 367
Created a new atom named: P within residue: .R< 367>
Created a new atom named: O1P within residue: .R< 367>
Created a new atom named: O2P within residue: .R< 367>
Created a new atom named: O3P within residue: .R< 367>
total atoms in file: 3005
Leap added 2880 missing atoms according to residue templates:
2880 H / lone pairs
The file contained 8 atoms not in residue templates
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Received on Wed Apr 04 2007 - 06:07:19 PDT
