I am trying to make the model for one of the protein by using a template. The template pdb file starts from 47th residue while in the sequence given in the fasta format for that pdb file, the amino acids start from first residue and instead of starting from M amino acid, it starts from SM. I had aligned that sequence with the sequence of my target protein using clustalW. While running the modeller, it is giving the following error-
"No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " A"; atom file name: ./filename.pdb"
I think I should modify the pdb file and replace the 47,48 and so on with 1,2...and so on. I don't know whether it would work or not.
Please give me your valuable suggestions.
First and foremost... Modeller does not take input sequences in Fasta format. It requires in PIR format. Secondly you need not have to renumber the residues.
For beginners I would suggest that you use GUI for modeller called EASYMODELLER. Its is opensource software. In this way you will not have to worry about complicated format conversions and writing Python script files to run modeller. EASY MODELLER is available at http://modellergui.blogspot.in/
Hope this will help...
Thank you for your suggestion. But there should be some troubleshoot for the above mentioned problem. If you have any idea, please help me go through. Your suggestions would be highly appreciated.
I was also not putting the fasta format. I just edited the existing example alignment file. First the alignment was done using clustalw and then it was inserted in the alignment file according to its alignment.
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