Hello Charles, The main thing which I want to include is the minimal distance between the helices when they lie on the surface of the micelle. Probably, lower bound distance restraints would be helpful. I could write a list where each long-range distance should not be closer than the diameter of the micelle (minus a term for the immersion depth of each helix), which seems to be the non-elegant way of doing this. Furthermore, the negatively charged headgroups of the micelle might be important if an electrostatic term is included in the force field.
Thanks for your comments! Franz "Charles at Schwieters.org" wrote on 19.11.09 23:20: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hello Franz-- > >> I want to set up a structure calculation run for a membrane protein in >> presence of an SDS micelle. I used PRE restraints and a minimal set of NOE >> data as well as chemical shift information. During the calculation there is >> no convergence to a single structure. I wondered if this might be due to the >> fact, that the PRE restraints are rather rong-range in nature. Therefore, >> the use of a micelle during the calculation might help to provide an >> 'alignment' frame for the protein which lies on the surface of the micelle. > > This sounds like a very expensive calculation which would likely > converge worse than if the micelle is omitted. What aspect of the > micelle would you like to include? There is likely a more efficient way > of doing this. > > best regards-- > Charles > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAksFxKoACgkQPK2zrJwS/lbyTQCeLc/ali9YQLb/tj6Zr61QyJSz > SKkAoIi2g+6U1jRoDTtNApo2J139Whal > =pvp6 > -----END PGP SIGNATURE-----
