the top of page 121 is pretty clear-
r1/r2/r3/r4 define the function used for the
restraint. those values are the distances
where the restraint function changes.
you determine the values based on what
distance range you want to penalize.
r1 and r4 are less important unless you
expect that the violations may become
large and you need a linear penalty instead
of harmonic- this is probably most useful
with nmr structure refinement.
between r2 and r3 there is no penalty,
so that could be the fluctuations you want
to allow or perhaps the uncertainty in
experimental data that you are using for the
restraint. it's hard to give one way to determine
these values since the restraints are used for so
many different purposes.
Kara Di Giorgio wrote:
> I've read that. It gives a lot of info about, if r2>r1 then this is
> used, etc, but no info about the meaning of the values of r1 or r2.
> How do you choose the values? What do the actual values mean?
>
> Kara Di Giorgio
>
> On Apr 13, 2005, at 10:06 PM, Furse, Kristina Elisabet wrote:
>
>> Kara-
>>
>> Have you read p. 121 of the amber8 manual? It describes how r1
>> through r4
>> control the restraint potential.
>>
>> Kristina
>>
>>
>> Quoting Kara Di Giorgio <kdigiorgio.sbcglobal.net>:
>>
>>> I'm trying to set distance restraints between the Ca and the O's of the
>>> protein.
>>>
>>> Any help is greatly appreciated!
>>>
>>> Kara Di Giorgio
>>>
>>> On Apr 13, 2005, at 2:18 PM, Carlos Simmerling wrote:
>>>
>>>> do you want positional restraints? in that case you don't
>>>> need the disang file. that's for distance, angle or dihedral
>>>> restraints. tell us what you are trying to restrain and we can
>>>> point you to the right spot...
>>>> carlos
>>>>
>>>> Kara Wald wrote:
>>>>
>>>>> I'm trying to restrain a Ca within a protein for a dynamics
>>>>> simulation and am having trouble formatting the DISTANG file.
>>>>>
>>>>> I've looked at the sample files in the manual and read the section.
>>>>> What are r1 through r4? In the manual, there is a blank listed next
>>>>> to them and I've found references to "should be formatted like
>>>>> r1through r4" but no info about what they stand for/mean.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Kara Di Giorgio
>>>>>
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>>>>
>>>>
>>>>
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>>
>>
>> -----------------------------------------------------------------
>> Kristina E. Furse
>> Department of Chemistry
>> Center for Structural Biology
>> Vanderbilt University
>> Email: kristina.e.furse.Vanderbilt.Edu
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Received on Thu Apr 14 2005 - 17:53:00 PDT
