Dear amber team
I am trying to change the end of my peptide chain (in pdb file)so i'll add
amide group (NH2) at the carpoxyl terminus of the peptide insread of one of
the oxygen atom attached to the carpoxyle carbon? but amber didn't accept
that every time it delete it and add OXT atom?
ATOM 3105 OD1 ASN P 5 41.098 65.202 -3.404 1.00 47.96
O
ATOM 3106 ND2 ASN P 5 43.323 65.656 -3.468 1.00 47.14
N
ATOM 3107 N TYR P 6 41.551 60.487 -6.012 1.00 24.72
N
ATOM 3108 CA TYR P 6 41.616 59.590 -7.164 1.00 22.15
C
ATOM 3109 C TYR P 6 40.774 60.234 -8.266 1.00 21.95
C
ATOM 3110 O TYR P 6 39.555 60.176 -8.207 1.00 21.25
O
ATOM 3111 CB TYR P 6 41.068 58.202 -6.866 1.00 21.39
C
ATOM 3112 CG TYR P 6 41.847 57.366 -5.863 1.00 19.06
C
ATOM 3113 CD1 TYR P 6 41.589 57.466 -4.512 1.00 16.12
C
ATOM 3114 CD2 TYR P 6 42.800 56.441 -6.274 1.00 15.31
C
ATOM 3115 CE1 TYR P 6 42.257 56.717 -3.628 1.00 15.10
C
ATOM 3116 CE2 TYR P 6 43.510 55.696 -5.390 1.00 13.45
C
ATOM 3117 CZ TYR P 6 43.226 55.805 -4.054 1.00 15.29
C
ATOM 3118 OH TYR P 6 43.914 55.071 -3.133 1.00 14.56
O
ATOM 3119 N PRO P 7 41.417 60.776 -9.285 1.00 21.63
N
ATOM 3120 CA PRO P 7 40.708 61.437 -10.395 1.00 21.38
C
ATOM 3121 C PRO P 7 39.731 60.470 -11.044 1.00 20.08
C
ATOM 3122 O PRO P 7 40.005 59.287 -11.207 1.00 18.00
O
ATOM 3123 CB PRO P 7 41.824 61.799 -11.375 1.00 23.11
C
ATOM 3124 CG PRO P 7 43.064 61.687 -10.604 1.00 25.67
C
ATOM 3125 CD PRO P 7 42.862 60.695 -9.527 1.00 23.44
C
ATOM 3126 OXT PRO P 7 38.590 60.992 -11.468 1.00 18.89
O
TER 3127 PRO P 7
END
Best Regards,
*Esam *
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Received on Tue Jun 28 2011 - 03:30:03 PDT
