Are there tools or scripts out there that can convert Modeller restraints (eg. rsr files) to Gromacs distance restraints? If not, how would you go at it?
Matthias -- Structural Bioinformatics and Computational Biochemistry Unit Dept. of Biochemistry University of Oxford http://sbcb.bioch.ox.ac.uk/schmidt.php
On 10/27/11 4:09 AM, Matthias Schmidt wrote: > Are there tools or scripts out there that can convert Modeller > restraints (eg. rsr files) to Gromacs distance restraints? If not, how > would you go at it?
The format is pretty simple, so it certainly wouldn't be that hard to do. The format is described at http://salilab.org/modeller/9.10/manual/node475.html
Note, however, that not all static restraints are distance restraints, and not all forms are the same (e.g. most are harmonic, but some are cubic splines). And some restraints such as DOPE are dynamic and not stored in the .rsr file.
The Integrative Modeling Platform, IMP, has an IMP.modeller module that converts all Modeller restraints to their IMP equivalents, so you could also use that Python code to help you. (Since it handles almost all restraint types, and also handles internal coordinates and dynamic restraints, it's a bit more involved.) See the load_static_restraints_file() method in the ModelLoader class at http://svn.salilab.org/imp/trunk/modules/modeller/pyext/IMP_modeller_init.i
Ben Webb, Modeller Caretaker