Tom Burghardt wrote:
I would like to make a DOPE profile for a modeled protein containing a
chemically modified side chain. I used the script suggested in the
Advanced Tutorial with the following lines to read the library files
containing information about the modified residue.
env = environ(restyp_lib_file='${LIB}/restyp_tom.lib')
env.libs.topology.read(file='$(LIB)/top_heav_tom.lib') # read topology
env.libs.parameters.read(file='$(LIB)/par_tom.lib') # read parameters
The DOPE profile is created by the script but the modified residue is left
out of the profile.
Any suggestions would be appreciated.
DOPE is a statistical potential, derived from the known distributions of standard residue types in PDB. Thus, by definition, it cannot tell you anything about non-standard residues; you would have to rederive the potential including examples of your modified residue, which is not a trivial task.
A 'regular' profile should work just fine, since the default (non-DOPE) potential acts on known _atom_ types.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage