Dear users,
When i load a pdb in xleap. I get the following message. But the atom names
in my pdb files especially for these residues are indeed unique. Kindly
write me what is going wrong. I am using amber9 and using ff99SB forcefield.
> b = loadPDB "/home/bala/ggp/ggp_b.pdb"
Loading PDB file: /home/bala/ggp/ggp_b.pdb
Enter zPdbReadScan from call depth 0.
-- residue 246: duplicate [ C] atoms (total 2)
-- residue 246: duplicate [ CA] atoms (total 2)
-- residue 246: duplicate [ N] atoms (total 2)
-- residue 246: duplicate [ O] atoms (total 2)
-- residue 247: duplicate [ C] atoms (total 2)
-- residue 247: duplicate [ CA] atoms (total 2)
-- residue 247: duplicate [ CB] atoms (total 2)
-- residue 247: duplicate [ CD] atoms (total 2)
-- residue 247: duplicate [ CG] atoms (total 2)
-- residue 247: duplicate [ N] atoms (total 2)
-- residue 247: duplicate [ O] atoms (total 2)
-- residue 248: duplicate [ C] atoms (total 2)
-- residue 248: duplicate [ CA] atoms (total 2)
-- residue 248: duplicate [ N] atoms (total 2)
-- residue 248: duplicate [ O] atoms (total 2)
ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
(same-name atoms are reduced to a single atom)
The following is the portion from the pdb for these residues
ATOM 744 N VAL G 245 86.769-152.726 108.476 1.00142.71
N
ATOM 745 CA VAL G 245 86.005-153.338 109.549 1.00143.44
C
ATOM 746 C VAL G 245 84.747-152.503 109.763 1.00143.75
C
ATOM 747 O VAL G 245 84.627-151.413 109.204 1.00143.15
O
ATOM 748 CB VAL G 245 86.821-153.377 110.853 1.00144.12
C
ATOM 749 CG1 VAL G 245 87.881-154.460 110.778 1.00144.77
C
ATOM 750 CG2 VAL G 245 87.479-152.032 111.086 1.00144.53
C
ATOM 751 N GLN G 246 83.808-153.006 110.557 1.00144.36
N
ATOM 752 CA GLN G 246 82.577-152.266 110.799 1.00144.77
C
ATOM 753 C GLN G 246 82.652-151.364 112.024 1.00144.15
C
ATOM 754 O GLN G 246 82.087-150.272 112.025 1.00143.24
O
ATOM 755 CB GLN G 246 81.392-153.227 110.918 1.00146.20
C
ATOM 756 CG GLN G 246 81.220-154.117 109.699 1.00148.95
C
ATOM 757 CD GLN G 246 81.195-153.327 108.400 1.00150.00
C
ATOM 758 OE1 GLN G 246 80.344-152.461 108.202 1.00150.67
O
ATOM 759 NE2 GLN G 246 82.136-153.623 107.510 1.00149.89
N
ATOM 760 N CYX G 247 83.338-151.814 113.069 1.00143.81
N
ATOM 761 CA CYX G 247 83.474-150.999 114.274 1.00143.17
C
ATOM 762 C CYX G 247 84.949-150.785 114.595 1.00142.65
C
ATOM 763 O CYX G 247 85.796-151.613 114.255 1.00142.71
O
ATOM 764 CB CYX G 247 82.810-151.662 115.485 1.00142.99
C
ATOM 765 SG CYX G 247 80.988-151.740 115.542 1.00143.43
S
ATOM 766 N THR G 248 85.247-149.676 115.262 1.00141.73
N
ATOM 767 CA THR G 248 86.613-149.336 115.640 1.00140.76
C
ATOM 768 C THR G 248 87.070-150.095 116.883 1.00140.31
C
ATOM 769 O THR G 248 86.258-150.456 117.731 1.00140.20
O
ATOM 770 CB THR G 248 86.725-147.838 115.923 1.00140.39
C
ATOM 771 OG1 THR G 248 86.168-147.112 114.824 1.00141.14
O
ATOM 772 CG2 THR G 248 88.169-147.433 116.094 1.00140.10
C
ATOM 773 N HIS G 249 88.375-150.325 116.991 1.00139.86
N
ATOM 774 CA HIS G 249 88.932-151.035 118.138 1.00139.38
C
ATOM 775 C HIS G 249 88.597-150.355 119.464 1.00137.88
C
ATOM 776 O HIS G 249 88.282-149.167 119.501 1.00138.46
O
ATOM 777 CB HIS G 249 90.449-151.170 117.990 1.00140.83
C
ATOM 778 CG HIS G 249 90.872-152.257 117.049 1.00143.17
C
ATOM 779 ND1 HIS G 249 90.448-152.316 115.739 1.00143.35
N
ATOM 780 CD2 HIS G 249 91.689-153.323 117.227 1.00143.40
C
ATOM 781 CE1 HIS G 249 90.986-153.371 115.151 1.00143.13
C
ATOM 782 NE2 HIS G 249 91.743-153.998 116.032 1.00143.09
N
Thank you,
Bala
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Received on Tue Jan 06 2009 - 15:32:09 PST
