Re: hydrogens in output structure

[sali AT rockvax.rockefeller.edu]

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 AT chemi.muni.cz
>        phone:  +420-5-41129 377
>        FAX:    +420-5-41129 506
>        http://www.chemi.muni.cz/~jiri 
> 


-- 
--
Andrej Sali, Assistant Professor
The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399
tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540
e-mail sali AT rockefeller.edu; http://salilab.org