I have been testing MODELLER with a ras-GDP template for inclusion of such a
'standard' nucleotide ligand as GDP. My most recent files are attached
(.ali, .top, .log, and template/model pdb files).
The problem: warnings (W>) in log file indicate lack of some parameters for
GDP in the par.lib file, even though GDP is included as a residue in the
res_type.lib. MODELLER adds some defaults values for the undefined
parameters, but clearly does not handle the GDP accurately since, in the pdb
model calculated, the guanine ring is nonplanar. I am not that familiar with
the format of the par.lib file. Is there a reasonable way to add parameters
to get the GDP ligand modeled properly?