Hello Rajbinder Kaur Virk-- > > In order to follow the symmetry-ADR method, following sequence of > protocol was followed: generate.inp > generate_template.inp > > randomchain.inp>refine.inp>rerefine.inp while using sum averaging > method. > > With the help of literature ( Unraveling the symmetry ambiguity in a > hexamer: Calculation of the R6 human insulin structure, Sean > I. O’Donoghue et.al & Calculation of Symmetric Oligomer Structures > from NMR Data, Seán I O’Donoghue and Michael Nilges) successfully we > were able to add NMR restrains into Molecular dynamics simulated > annealing of a symmetric homo-trimer. We have achieved minimum > energy structures. > > However, there must be a single metal atom bound to the three homo > trimers at the center. I am unaware that at which step of the > protocol I must include the metal such that oligomers of that metal > itself does not form. It would be very helpful if someone can > please guide me through. I am little stuck as not fully aware of > the calculations by XPLOR, I thank you in anticipation. >
Your approach uses the old XPLOR interface which has been superseded by the Python interface. For this case, it is almost certainly better to use the SymSimulation strict symmetry facility discussed in the Protein Science, 27, 26 (2018) paper. I believe your specific issue is due to an atom which lies on a symmetry axis. Using the current SymSimulation implementation, it would probably be easiest to simply replicate this atom, but disable nonbonded interactions between the copies. Perhaps you can implement this in the old interface if other approaches don't work out. [Also, please use the new [email protected] address for future posts.] best regards-- Charles ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
