Hi Bozidar,
Here's what my top file looks like.
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE #Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 #uncomment to produce a large log file SET ALNFILE = 'hpabc.ali' #alignment filename SET KNOWNS = '1G9L' # codes of the templates SET SEQUENCE = 'wPABC' # code of the target SET ATOM_FILES_DIRECTORY = '.' #directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of > Stephane Coillet-Matillon > Sent: Tuesday, March 19, 2002 5:32 PM > To: modeller_usage@salilab.org > Subject: pdb format > > > > Hello Modellers, > > I've been trying to run my first modelling, but cannot get any model so > far. Instead, the log file tells me: > > Read the alignment from file : hpabc.ali > Total number of alignment positions: 144 > # Code #_Res #_Segm PDB_code Name > ------------------------------------------------------------------------ > ------- > 1 1G9L 144 1 1G9L PABC > 2 wPABC 72 1 wPABC PABC > > TOP_________> 121 107 CHECK_ALIGNMENT > > check_a_343_> >> BEGINNING OF COMMAND > openf5__224_> Open 11 OLD SEQUENTIAL ./1G9L.atm > rdpdb___303E> No atoms were read from the specified input PDB file: > 1) Possibly because an incorrect/non-existent PDB file > is specified. > 2) Possibly because the segment is specified incorrectly > in the alignment file or by the TOP variable MODEL_SEGMENT. That is, the > beginning residue number and/or chain id in MODEL_SEGMENT may not be > found in the input PDB file; MODEL_SEGMENT:1 : > To find out more, switch on maximal output by 'SET > OUTPUT_CONTROL = 1 1 1 1 2' rdabrk__288W> Protein not accepted: 1 > rdabrk__290E> Number of residues in the alignment and pdb files are > different: 144 0 > For alignment entry: 1 recover > ____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > My alignment file is: > > >P1;1G9L > structureN:1G9L:1 : :144 : :PABC:homo sapiens: : > GPLGSAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS > APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA > VLQAHQAKEAAQKAVNSATGVPTV* > >P1;wPABC > sequence:wPABC:1 : :144 : :PABC:wheat: : > --------------------------------------------------EPLTASMLAS > APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVA > VL----------------------* > > Which I trust is the right way to do it. > The top file has nothing that deviates from the example file. My pdb > file was just renamed from 1G9L.pdb to 1G9L.atm, its content was not > edited or changed, and it was located in the right directory. > > So what am I missing there? > > Any suggestion welcomed! > > Thanks, > Stephane >