Hello Narendra-- > >> I am calculating peptide structure that bound to the nano-particle > >> surface > >> in aqueous media by using XPLOR NIH.I have an unnatural amino acid(DOPA) > >> in my peptide sequence, So I modified protein force fields of DOPA > >> residue > >> accordingly.But the problem is after the annealing and refinement MD > >> runs > >> the output of average PDB file looks like N-terminal hydrogen and Serine > >> OH groups forming H-bonding with neighbor amino acids (looks like a > >> cyclic > >> peptide). > >> > > > > I will need a bit more information to figure out what the problem is, > > and how to solve it. First, I'll need a PDB which displays the problem > > (and why you think that this hydrogen bond should not exist). To solve > > any problem, I'll probably need a bit more information, such as the > > topology and parameter files for DOPA. > > > Thanks for your response.I attached PDB file which displays the problem > and topology, parameters for DOPA (DAH) residue to this e-mail. >
I see that the first residue makes four hydrogen bonds in this structure. Does the structure satisfy the experimental restraints? Do the other structure metrics (bonds, angles, Ramachandran, clashes) look ok? Why does the structure bother you? best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
