Hi modellers, I am new to this list and to modeller too. I was wondering that anybody faces the problem connected with max_pdf error. I have submitted modeller a job to model a protein of around 1200 residues. In the log it says that, >>summary of failed models 1fdx.B999900001.PDB obj.func. (109595.656) exceeded max_molpdf (100000.000). I don't know what is meant by max_molpdf. How should i proceed from this point? Thanks in advance.
With best regards, P.Balamurugan
Yours truly, P.BalaMurugan.
-------------------------------------------------- "Science is built up of facts, as a house is built up of stones,but an accumulation of facts is no more a science than a heap of stones is a house"-Henri Poincare
Bala Murugan wrote: > I am new to this list and to modeller too. > I was wondering that anybody faces the problem connected with max_pdf error. > I have submitted modeller a job to model a protein of around 1200 residues. > In the log it says that, > >>summary of failed models > 1fdx.B999900001.PDB obj.func. (109595.656) exceeded max_molpdf (100000.000). > I don't know what is meant by max_molpdf. How should i proceed from this > point?
max_molpdf is a maximum value for the objective function, used to discard really bad models. See http://salilab.org/modeller/8v2/manual/node44.html You can increase it by setting a.max_molpdf before you call a.make(), but this error is usually an indication of your initial model being very poor. You should examine the .ini file; perhaps your templates are not well aligned.
Ben Webb, Modeller Caretaker
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Bala Murugan -
Modeller Caretaker