Hello Rajbinder--
> > I intends to use XPlOR-NIH to perform molecular dynamics-simulated annealing > protocol in order to perform NMR-refinement of a metallopeptide with an > unusual set of aminoacid. > The forecefield parameters for the same were generated by using mcpb.py script > of amber and the required .prmtop and inpcrd files were generated. Thereafter > it was converted to xplor compatible psf files. However, on running the > simulated annealing protocol many parameters eg bond length energy are still > missing. > According to the following link the amber force field can be used in Xplor > http://ambermd.org/xplor-nih.html > However, I am not sure how, It would be very helpful if please somebody can > guide me through this. > I suspect that you will need to specify topology and parameters files for the rest of the protein. You probably should obtain up-to-date files, but Xplor-NIH ships with some of these in toppar/topamber.inp and toppar/parmallh3x.pro. However, unless you have a particularly good reason to use Amber parameters, I suggest that you instead generate Xplor-NIH-compatible parameters for your non-natural residues, perhaps with the aid of PRODRG (http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg) best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
