Dear All,
I do have some errors with pdb file which was resolved but I am stuck now on
the following error in xleap causing hinderance to proceed
Added missing heavy atom: .R<CLEU 174>.A<OXT 20>
Created a new atom named: CO within residue: .R<CAT 175>
Added missing heavy atom: .R<CAT 175>.A<C0 1>
total atoms in file: 1115
Leap added 1006 missing atoms according to residue templates:
9 Heavy
997 H / lone pairs
The file contained 1 atoms not in residue templates
Previously it was 3 atoms not found in residue templates resolved by manual
rectification in pdb file. part of my pdb file is........
ATOM 631 C ILE 170 -0.169 27.458 19.602
ATOM 632 O ILE 170 0.758 28.241 19.412
ATOM 633 N VAL 171 -1.248 27.434 18.811
ATOM 635 CA VAL 171 -1.444 28.398 17.775
ATOM 637 CB VAL 171 -1.375 28.200 16.281
ATOM 639 CG1 VAL 171 -0.007 27.587 15.946
ATOM 643 CG2 VAL 171 -2.520 27.259 15.851
ATOM 647 C VAL 171 -2.832 28.906 18.053
ATOM 648 O VAL 171 -3.769 28.122 18.196
ATOM 649 N THR 181 -0.160 21.431 20.978
ATOM 651 CA THR 181 0.495 20.175 20.844
ATOM 653 CB THR 181 1.764 20.236 20.044
ATOM 655 OG1 THR 181 2.696 21.102 20.675
ATOM 657 CG2 THR 181 1.435 20.749 18.630
ATOM 661 C THR 181 0.846 19.696 22.214
ATOM 662 O THR 181 1.192 20.476 23.100
ATOM 663 N ASN 182 0.715 18.376 22.414
*and lower portion*
ATOM 1834 OE2 GLU 354 21.599 44.549 8.829
ATOM 1835 C GLU 354 20.553 38.777 7.583
ATOM 1836 O GLU 354 21.341 37.833 7.594
ATOM 1837 N LEU 355 19.484 38.797 6.762
ATOM 1839 CA LEU 355 19.280 37.698 5.857
ATOM 1841 CB LEU 355 17.827 37.504 5.366
ATOM 1844 CG LEU 355 16.856 36.992 6.446
ATOM 1846 CD1 LEU 355 17.160 35.544 6.859
ATOM 1850 CD2 LEU 355 16.894 37.906 7.659
ATOM 1855 C LEU 355 20.089 37.974 4.634
ATOM 1856 O LEU 355 20.862 38.928 4.576
TER 1857 LEU 355
HETATM 1858 CO CAT 357 9.614 26.052 22.921
TER 1859 CAT 357
HETATM 1860 P PAT 358 12.189 24.618 25.115
TER 1861 PAT 358
Rest I am waiting for any suggestion and will be thankful for your reply.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 22 2010 - 09:30:04 PDT
