Hey Ben,
I've been generating some models of some cytochrome proteins with heme. I have generated ~6 structures that are all fine but the next two have the heme placed out in space relative to the protein. I have seen this before but have put it down to user error. Now I'm not so sure its me as I have been simply replicating the input files. Any suggestions? (I don't what to post files to bulletin board but can send direct (if needed)).
J
_________________________________ Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall
Ph: +64 3 479 7293
On 6/14/14, 7:53 PM, Joel Tyndall wrote: > I’ve been generating some models of some cytochrome proteins with heme. > I have generated ~6 structures that are all fine but the next two have > the heme placed out in space relative to the protein. I have seen this > before but have put it down to user error.
This would be the case if there were no restraints on the heme, which will happen if you don't have any template protein within the cutoff distance: http://salilab.org/modeller/9.13/manual/node70.html
You might sometimes get models that look OK because the heme is trapped purely by VDW interactions, or it just didn't have to wander off too far.
Ben Webb, Modeller Caretaker
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