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. best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
