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Hello Gary-- > > many moons ago (well at least two years) you alluded to how to calculate > structures of symetric dimers with marvin: > > > > I plan to also perform calculations for a dimer model system > > > (modeling monomer > > > interactions in the solid state), for this system PASD should be > > > able to > > > identify which contact are intra- and intermolecular - I hope... > > > Can I use an NCS (to enforce identity of the monomers) potential > > > energy term as > > > well from the tcl interface? > > > What about distance difference potential to enforce NMR equivalence > > > of the > > > monomers? > > > > You can add any xplor-nih potentials you like during a Marvin > > calculation. I've > > done structures with NCS and distance symmetry. It's just a matter > > of setting up the > > potentials at the beginning of the sa_pass*.tcl scripts, using the > > classic xplor language > > enclosed in a TCL XplorCommand " ... " call. When you're ready to > > try, let me know and > > I'll post in more detail. > > > I'm not certain that John ever successfully treated a symmetric dimer. I have found examples of adding NCS and distance symmetry restraints - which will be essential. Add the code snippet below to sa_pass2/3.tcl, and modify the scripts, adding ncs and distSymm to the potsToUseDuringRandomization/Annealing arguments of pass2/3 in the two respective scripts. Please let me know how it goes. Charles # # set up the NCS restraints # set ncs [create_XplorPot NCS] XplorCommand "ncs restraints group equiv (segid A) equiv (segid B) weight 1 end end" # # set up the distance symmetry # set distSymm [create_XplorPot NOE] XplorCommand "noe class symm @DistanceSymmetry.tbl potential symm symmetry scale symm 1.0 soexponent symm 1 rswitch symm 0.5 asymptote symm 1.0 end" -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.9 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAko6UBMACgkQPK2zrJwS/lZTAACfXwP2lxRB9DY6NciJaY4Oqhen ktoAnjRBLW+/lo9se6L8a7H6ZOxtJyHV =8NLT -----END PGP SIGNATURE-----
