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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?
Thanks,
Tom
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Attachment:
ras3.tar.gz
Description: GNU Zip compressed data