AMBER Archive (2005)

Subject: AMBER: amber question about leap

From: du yongchun (phoebus2008_at_hotmail.com)
Date: Thu Jun 02 2005 - 00:12:12 CDT

hi,amber
  I use leap in AMBER 7 to read the following PDB file:tyr.pdb
--------------------------
ATOM 1 N TYR A 232 50.415 20.722 33.620 1.00 88.79
 N
ATOM 2 CA TYR A 232 49.303 20.256 32.736 1.00 90.26
 C
ATOM 3 C TYR A 232 48.564 21.407 32.050 1.00 87.43
 C
ATOM 4 O TYR A 232 48.222 22.407 32.685 1.00 86.29
 O
ATOM 5 CB TYR A 232 48.298 19.423 33.543 1.00 90.63
 C
ATOM 6 CG TYR A 232 47.027 19.092 32.785 1.00 90.08
 C
ATOM 7 CD1 TYR A 232 47.070 18.376 31.588 1.00 89.49
 C
ATOM 8 CD2 TYR A 232 45.782 19.506 33.261 1.00 89.92
 C
ATOM 9 CE1 TYR A 232 45.906 18.084 30.882 1.00 88.07
 C
ATOM 10 CE2 TYR A 232 44.610 19.220 32.563 1.00 88.75
 C
ATOM 11 CZ TYR A 232 44.679 18.508 31.374 1.00 88.31
 C
ATOM 12 OH TYR A 232 43.525 18.228 30.676 1.00 88.07
 O
------------------------------
xleap
>source leaprc.ff02
>x=loadpdb tyr.pdb
the output is as the follewing:
  Loading PDB file : ./tye.pdb
     Added missing hervy atom : .R<CTYR 232>.A<OXT 22>
     total atoms in file:12
     ..............
the residue name in the pdf file is TYR ,but in xleap ,it changes to CTYR
and add an atom OXT.I don't know why it is.Can you tell me why and how can
I modify it.Thanks!
                                                                            
         Du Yongchun
                                                                            
         5.31,2005

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