Dear Modeller users: Is there any way how to generate homology model with hydrogen atoms included in the output structure. we tried using the template structure with hydrogens and 'SET HYDROGEN_IO = on' in the top file, but the output structure was again without hydrogens.
Thank you very much for your advice. Best regards, Jiri
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Dr. Jiri Damborsky Laboratory of Biomolecular Structure & Dynamics Masaryk University Kotlarska 2 611 37 Brno Czech Republic
e-mail: jiri@chemi.muni.cz phone: +420-5-41129 377 FAX: +420-5-41129 506 http://www.chemi.muni.cz/~jiri
Hi,
You also need to tell MODELLER to read the topology and parameters libraries with hydrogens, and you need to tell it you are using hydrogen topologies. All this is achieved by
READ_TOPOLOGY FILE = '$(LIB)/top_allh.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' SET TOPOLOGY_MODEL = 1
somewhere before CALL ROUTINE='model'.
Best, Andrej
> > Dear Modeller users: > Is there any way how to generate homology model with hydrogen > atoms included in the output structure. we tried using the template > structure with hydrogens and 'SET HYDROGEN_IO = on' in the top > file, but the output structure was again without hydrogens. > > Thank you very much for your advice. > Best regards, > Jiri > > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > > Dr. Jiri Damborsky > Laboratory of Biomolecular > Structure & Dynamics > Masaryk University > Kotlarska 2 > 611 37 Brno > Czech Republic > > e-mail: jiri@chemi.muni.cz > phone: +420-5-41129 377 > FAX: +420-5-41129 506 > http://www.chemi.muni.cz/~jiri >
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