Hi All, I am attempting to perform some SA on a complex of two proteins, one has an elongated shape and the other is roughly spherical. If I do not include a collapse term, the two proteins end up inside each other and all restraints are thus violated and the VdW energy is huge. If I include a collapse term for the entire complex, the proteins remain far apart, as they are randomly placed at the beginning of the run. I have also try to separate the complex into three separate roughly spherical domains, to then calculate the Rgyr for each domain and then to include these in three separate collapse assign statements in old xplor language, when I do this the collapse term becomes NaN as does the gradient and the Epot and Ekin terms. How can I handle this sort of complex and get the proteins to move close together without getting too close. Do I need an Rgyr term, if so, what form should it take? In the SA run bonds, angles, impropers, VdW and PRE terms are all included in the XplorPot.
Any ideas? Many Thanks and Kind Regards Simon Skinner -- Simon P Skinner Protein Chemistry Group Leiden Institute of Chemistry, Universiteit Leiden Phone: +31 71 527 6089 / Fax: +31 71 527 4349 E-mail : skinnersp at chem.leidenuniv.nl
