ADL: Can't find or open AD4.1_bound.dat

Ruth Huey rhuey at scripps.edu
Mon Jan 12 09:50:23 PST 2009


Hi Maura and Steffen,

AD4.1_bound.dat is the parameter file to use if you want to run 
autodock4.1.
The version which is on the autodock website (autodock.scripps.edu) is 
the one-to-use because it includes this important line:

FE_unbound_model unbound_same_as_bound

The other important difference in setting up a parameter file to run 
autodock4.1 instead of autodock4.0 is that the keyword 
"compute_unbound_extended" is necessary in a dpf for autodock4.0 but 
should not be in a dpf for autodock4.1.
 
    Ruth



Steffen Moeller wrote:
> Hi Maura,
>
> Maura Catherine Mooney wrote:
>   
>> I'm not sure what would cause this file to be unrecognized/unopenable,
>> but I noticed that the sample AD4.1_bound.dat file on the autodock
>> website is slightly different.  Have you any ideas?  I was thinking
>> of editing my file to corroborate with the sample file on the internet,
>> but would you just recommend a fresh install?
>>     
>
> there is some rule of thumb that 20% of the programming time is spent for getting the
> basic functionality established, which feels like 80% of the whole thing. And 80% of the
> time goes up for checking what could all go wrong and other beasts that ... just hurt.
> Those 80% rarely get completed and you may by chance have just hopped on such an island of
> dysfunctionality.
>
> There is the possibility that I am just waisting your time, but when something weird
> happens in IT, and a reinstallation does not take long (15-30 minutes is not long), then
> just go for it. If it then works - fine. If you want to be good, then try reproducing that
> behaviour with the new version and report how to do that. If the new version does not
> work, then the problem is not (primarilty) with the MGLTools or you have not removed (or
> at least renamed so it is no longer found by accident) your old version.
>
> Wishing you more luck than before and enjoy the new version (the beta I mean) should the
> problem later turn out to be cause by something else.
>
> Steffen
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>   



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