Hello Xiaogang-- > > I try to do structure calculation of this cyclic peptide use > the attached "random.inp" file which I modified from the same file > of 'xplor-nih/tutorial/nmr' folder. I found that in the calculated > PDB files, the atoms of DAP residue may get too close to each other > which impede the formation of the right bond topology, and the > peptide bond between CG of ASP and NZ of DAP are easily broken ( as > in the pdb file attached). I guess I need to define the DAP residue > and CG-NZ peptide bond somewhere before the structure > calculation. Do you have any suggestion about this? >
Do you load parameters for DAP? This needs to be done, as it is in the gen.py file I sent you. Also, I strongly suggest that you stick with the Python interface, as it is simpler and has many more features. A good starting point is in the gb1_simple subdirectory of the hands-on tutorial available from http://nmr.cit.nih.gov/xplor-nih/doc/current/ best regards-- Charles _______________________________________________ Xplor-nih mailing list [email protected] https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
