Dear Modellers,
I am having difficulty getting modeller to run to completion. Here is my directory contents, my top and ali files, and an excerpt from my log file. I have also attached my complete pdb file and log file. I would greatly appreciate any suggestions as to how to get this modeller job to run to completion.
My directory contents:
1g2a.atm.old 1g2i_b.pep comppdb monomer.msf park7-ig2i_b.pair park7.ssearch 1g2i.pdb 1g2i_b.tfa model-monomer.log monomer.ps park7-ig2i_c.pair xa.nrl3d.list 1g2i_a.pep 1g2i_c.pep model-monomer.top nm_007262.rsf park7.gap 1g2i_a.tfa 1g2i_c.tfa monomer.ali np_009193.rsf park7.pdb.netblastp 1g2i_b.pdb 1ga2.atm monomer.list park7-ig2i_a.pair park7.pep
My top file
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'monomer.ali' # alignment filename SET KNOWNS = '1ga2' # codes of the templates SET SEQUENCE = 'prk7' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # 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
My alignment file
C; alignment >P1;1ga2 structureX:1ga2:1 : :166 : :Protease:Pyrococcus Horikosh: 2.00:-1.00 ---MKVLFLTANEFEDVELIYPYHRLKEEGHEVYIASFE-RGTITGKHGYSVKVDLTFDK VNPE-EFDALVLPGGRAPERVRLNEKAV--SIARKMFSEGKPVASICHGPQILISAGVLR GRKGTSYPGIKDDMINAG-VEWVDAEVVVDGNWVSSRVPADLYAWMREFVKLLK------ ----------* >P1;prk7 sequence:prk7:1 : :189 : :park7:human: 2.00:-1.00 MASKRALVILAKGAEEMETVIPVDVMRRAGIKVTVAGLAGKDPVQCSRDVVICPDASLED AKKEGPYDVVVLPGGNLGAQ-NLSESAAVKEILKEQENRKGLIAAICAGPTALLAHEIGC GSKVTTHPLAKDKMMNGGHYTYSENRVEKDGLILTSRGPGTSFEFALAIVEALNGKEVAA QVKAPLVLKD*
The error message
Read the alignment from file : monomer.ali Total number of alignment positions: 190
# Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1ga2 166 1 1ga2 Protease 2 prk7 189 1 prk7 park7 TOP_________> 121 107 CHECK_ALIGNMENT
check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1ga2.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: 166 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
The complete log file and pdb file are attached.
Thanks and best wishes, Rich -------------------------------------------------------------- Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Medical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/
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