Re: [modeller_usage] DOPE profile

[Modeller Caretaker <>]

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
--
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