-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
Hello Yi-- > > Thank you very much for your previous reply. The side chain > minimization went well now. Here is another issue, I have an oligomer > model generated according to symmetry. The core of the model is quite > crowded due to overlapping of a helical component. I would like to > perform rigid body refinement of the modeled structure without > experimental determined restraints. To do this, I need to fix the > peripheral part of the protomer and group the central alpha helix, > allowing the central alpha helix to move apart from each other during > energy minimization. The script I use is 'sa_mef_dipo.inp' from the > eginput/ mef_dna. How should I express the 'fix and group' in this > macro? (The expression in 'anneal.py' does not work here.) Because that old XPLOR script was written before the IVM was added, it does not support rigid body grouping in the same was as in the Python scripts (or using the dyanmics internal statement in the old XPLOR language). My advice is to switch to a different base script for this work. > > Another problem is that during minimization, the central helix should > not be thrown out from the core, can the script achieve this without > experimental restraints? Should I modify the simulation parameter such > as temperature, step, etc. and how? > If the nonbonded (vdw) energy term is enabled, the core portion should not move through other atoms to escape. However, if strain is too large I suppose it is possible- in this case, you might add a restraint to a subset of core atoms specifying that they move a bounded amount from their initial positions. This can be achieved with a PosDiffPot in the Python interface. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkzJksAACgkQPK2zrJwS/lbI4wCdFArPOmiw+POdFhNZMg5HMheQ gJUAnRmHgRP5FfiglH+xnrzfqFQQ8Fo+ =wBDg -----END PGP SIGNATURE-----
