leap does not know what residue "CAT" is. you need to fix this by changing
the name, or by building a library file. look at the tutorials for help on
new residues. we can't really help since we don't know what CAT is. same for
PAT.
On Mon, Mar 22, 2010 at 12:11 PM, sikander azam <syedazam2008.gmail.com>wrote:
> 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.
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Received on Mon Mar 22 2010 - 09:30:05 PDT
