I have just finished modeling TvLDH, following the example given in the paper "Comparative Protein Structure Modeling with MODELLER: A Practical Apporach". Methods in Enzymology. (submitted), by Andràs Fiser and Andrej Sali (http://salilab.org/modeller/methenz/). I have had a few problems running some of the scripts, but I have mainly been able to over come most of these.
I have, however, picked up a couple of problems :
1) The results I obtained from the 'align2d.top' script were slightly different from that reported in the paper, and those on the web-page quoted above (my alignment is attached
). This, of course, means that the resulting models are slightly different.
2) The structure file 4mdh.pdb contains a residue coded ACE, numbered resdue 0. This is an acetylated (acylated ??) N-terminus. However, 'align2d.top' appears to recognize this as a GLY, which is entered into the alignment files. This, of course, causes a problem in the final modeling, as the ACE residue is not recognized and the run fails. Editing the PIR alignment file to correct this (remove the G and change the 0 to 1).
3) Throughout the procedure, I had to use the PDB file 4mdh.pdb - for the template comparisons and alignments. However, I had to rename this file 4mdhA.pdb for the modeling - presumably because that is the sequence name given in the alignment file. Is there any way to prevent having to do this ?
Could someone explain the above problems.
I am using MODELER6v2, on a Mac PowerBook G4, running OS X/Darwin (10.1.5).