Hi,
It's hard to help you without looking at your .top file.
Thanks, Bozidar
-----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