Hello, My question concerns the 'best' way to treat the terminal groups for a protein that is missing residues at both termini, e.g. a 530 residue protein where only residues 15-512 are present in the pdb.
My thoughts are that assigning charges to the end groups will result in areas of charge in regions where there may not be any in the native protein and could lead to unknown artifacts. Another option would be to 'cap' or add a blocking group on the end of the protein chain, e.g. ACE, which introduces a group that is non-native to this region of the protein. Or treat the end groups neutrally. I have looked through the literature and while I can find examples of MD being carried out with structures with missing residues at the termini, but I cannot find any description of how these groups are treated. I would appreciate some views on this. N.B. The protein I am wishing to study is catalytically active and therefore I have confidence that these missing residues have no effect on the activity of the protein. Many thanks, Jo
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
