On 3/26/17 12:39 PM, Quin K wrote:
Thank you for the reply. I have another question. I used MODELLER on Chimera to fix the protein and found that there were significant visible changes to structure of protein. I'm not sure whether to use the old protein or the fixed one. Does it really matter that I used unfixed protein if the structure of binding site(s) and important chain features remain the same ? For the 50 ns MD simulation I never fixed the protein.
This all depends on what "fixed" means. Were there missing residues? Clashes in the structure? In the case of the former, without a "fix" then the missing residues will cause lots of problems. In the case of the latter, energy minimization is usually sufficient to alleviate any problems.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
