[MMTK] Problems with loading some PDF files

Новиков Глеб 0wn3r at bk.ru
Wed Oct 12 18:58:52 UTC 2011


Dear MMTK users!


I've forsed with some problem during loading of my pdb structure to the MMTK.

First of all I operate with full atomic models of my proteins obtained by the homology modelling teqnique. ( see atached example )

When I've tried to load this structure to the MMTK i've obtained error message 

IOError: Atom H of PDB residue VAL not found in residue Val of object .Val45

but Val45 ( as other residues in this structure) consist of all atoms- e.g


ATOM    674  N   VAL    45      30.950  51.650  51.300  1.00  0.00
ATOM    675  H   VAL    45      30.310  50.880  51.110  1.00  0.00
ATOM    676  CA  VAL    45      31.660  51.710  52.580  1.00  0.00
ATOM    677  HA  VAL    45      31.420  52.670  53.040  1.00  0.00
ATOM    678  CB  VAL    45      31.160  50.580  53.510  1.00  0.00
ATOM    679  HB  VAL    45      31.220  49.640  52.970  1.00  0.00
ATOM    680  CG1 VAL    45      31.990  50.450  54.790  1.00  0.00
ATOM    681 1HG1 VAL    45      31.590  49.640  55.400  1.00  0.00
ATOM    682 2HG1 VAL    45      33.010  50.210  54.540  1.00  0.00
ATOM    683 3HG1 VAL    45      31.950  51.380  55.360  1.00  0.00
ATOM    684  CG2 VAL    45      29.710  50.840  53.940  1.00  0.00
ATOM    685 1HG2 VAL    45      29.370  50.040  54.590  1.00  0.00
ATOM    686 2HG2 VAL    45      29.650  51.790  54.470  1.00  0.00
ATOM    687 3HG2 VAL    45      29.070  50.880  53.070  1.00  0.00
ATOM    688  C   VAL    45      33.180  51.660  52.380  1.00  0.00
ATOM    689  O   VAL    45      33.910  52.490  52.930  1.00  0.00

It seems that MMTK could not find hydrogens like 1HG1 2HG1 3HG1 etc

How I can add this atoms to MMTK database ? Or it'll be also also very comfortable that it'd be an apperation wich modify PDB to the suitable form ( e.g gromacs deleate all hydrogens and then build it at once)

Thank you for your help,

Gleb
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