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Hello Jie-rong-- > Instead of getting a refined structure, I am trying to have some sets or > contacts of conformation in a denatured protein with PRE restraints. One of > the currently used methods is applied in Michele Vendruscolo's group (e.g. > Dedmon et al, 2005 JACS, 127, 476-477). They calculated up to 20 copies of > extended protein together with long distance restraints by means of CHARMM > program. This sort of method depends critically on modelling, so you need to be careful to use a realistic force field properly including solvent effects. > One similar way in Xplor should be "ensemble.inp", I think. That script is not appropriate for extended structures with few restraints: there are no solvent effects included and electrostatics are disabled. > However, there is no "ensemble" parameter in PMAG (as in ensemble.inp "NOE > ensemble on end end") if I want to use delta R2 directly. If I want to > convert PRE into distance, it is also troubled me, because I am not sure > whether one can use the same energy function correctly. To refine directly against PRE, please use the Python module prePot, as in http://spin.niddk.nih.gov/clore/Software/pre_distribute.tar.Z > For example, > equation (18.6) in the Manual (potential = biharmonic) and equation (13) in > Iwahara 2004 JACS, is that possible convert the standard error of delta r2 > into upper bound and lower bond limits? That work did not convert PRE data to distance bounds. > > Besides, the script from Iwahara 2004 JACS is simulated annealing with > multiple ligand to average the conformation ensemble, right? I am wondering > where the ensemble calculation is called in this script, and in which kind of > restraint, in dintance or in relaxation rate? (as equations (13) (15) in > Iwahara 2004 JACS) That work directly refines against PRE data, as in the script cited above. In these scripts, the ensemble was built manually in the PSF. Since you're trying to simulate a partially-structured protein, you will have to modify the scripts appropriately to properly include solvent at an appropriate temperature. hope this helps-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD8DBQFIBLV6PK2zrJwS/lYRAsjbAJ0cwkqwo9ZOI26wFFz+xdGEGRRFLACZAZ+p nvw5EbGTvrgvWHwO6jsvtOI= =m6TZ -----END PGP SIGNATURE-----
