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
On Mon, Jan 19, 2004 at 05:18:14PM -0500, Thomas Duncan wrote: > 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?
Modeller uses CHARMM topology and parameter files. It includes some of the CHARMM22 forcefield, but not every residue type is fully modeled, so in this case you'll probably have to write your own parameters, or use the BLK residue type. See http://salilab.org/modeller/FAQ.html#17 for an overview, or consult the CHARMM documentation itself at http://www.charmm.org/
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Thomas Duncan