I'm reproducing [because I want to compare the results to another system] previously published work on a cytochrome C- neuroglobin complex. The protein-protein docking was done with freeware & that work didn't require a scoring function outside the one that came with that software. However, I'm thinking of equilibrating the structure from the docking software with MD & using MMPBSA to compute the delta G of interaction for this system as well as the one I want to compare to it. I have an input pdb structure arranged as cytochrome coords-TER-cytochr. heme-TER-neurgl-TER-neur heme. I've also tried it w/out the TER between globin & its respective heme, with identical results. I can easily use sleap to create a prmtop/inpcrd set. However, when I try to use ante-MMPBSA using a receptor_mask ":1-105" I get an error message regarding the C-terminal residues on each of the globin proteins. The error is that there's an extra OXT in each C-terminal residue. I suspect this may be because residue 105 is the heme & res
idue 104 is the C-terminal protein residue. I'm not at all interested in the protein/heme part of the interaction; I want the globin/globin interaction. Since the edges of the hemes are close to each other in the docked pose, I can't just ignore them. Is there a way to set this up with MMPBSA?
Thanks!
Irene Newhouse
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Received on Thu Oct 06 2011 - 16:30:04 PDT
