I simulated two different protein one which is a crystal structure and other is homology model at 303.15K for 20ns. Both the protein share a sequence similarity i.e. 98%. The script file is also alike. But the protein with crystal structure does not diverege to higher RMSD but on the other hand one with homology model diverges to higher RMSD (4.0 A).
I have also conducted energy minimization for the HM prior to simulation.
Hello,
Such phenomenon is to be expected on homology proteins, perhaps there are some issues with secondary structures or bumps due to the initial structure. If you have access to YASARA2 forcefield you could try optimizing your structure with it. If not you could use an extended minimization and restrained equilibration prior to productions runs. Still, as I said 4.0 A for RMSD isn't that much; you should check for other metrics such as RMSF, radius of gyration or plain visualization to see if something is really wrong with your system.
On the other hand, if you are describing a difference of 4.0 A between systems; this can still be totally normal depending on the size of the protein. With that said you could double check your homology protocol, perhaps there is a better template to use for the model.
Finally your could also review your protein with SAVES (https://servicesn.mbi.ucla.edu/SAVES/), for a more robust sanity check.
Hope this helps
Thanks, I have YASARA2 forcefield. should i choose that for simulations otherwise how do i optimize the HM structure.
There is a macro in YASARA that can do this optimization for you. If the values for the model are still of concern you can use the aforementioned macro as base to optimize your model further. If you still see important deviations I strongly suggest a template change.
Regards
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