Re: [modeller_usage] set topology for autobuilder.

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 03/19/2010 02:04 AM, Knut J Bjuland wrote:
> I used thesse commando to set toplogy information when doing an
> alignment. BUt it did work when I wanted to build it. What kind of
> command should I invoke to add thesse information in the build phase of
> modeller.
>
>
> env.libs.topology.read(file='$(LIB)/top_allh.lib')
> env.libs.parameters.read(file='$(LIB)/par.lib')

If you want to build an all-atom model, you can just use the allhmodel 
class rather than automodel. It will handle everything automatically for 
you (it also turns on env.io.hydrogen so hydrogen atoms in your 
templates are read in).

Otherwise, you can assign to toplib and parlib in your automodel object 
to specify files to use:

a = automodel(...)
a.toplib = '${LIB}/top_allh.lib'
a.parlib = 'my_parameters.lib'
a.make()

	Ben Webb, Modeller Caretaker
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