AMBER Archive (2005)

Subject: Re: AMBER: Formatting a restraint file

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Thu Apr 14 2005 - 11:25:18 CDT

I think you explained it. I guess the missing info was that they are
DISTANCES. I wasn't sure what the numbers meant.

Thanks,

Kara Di Giorgio

On Apr 14, 2005, at 9:13 AM, Carlos Simmerling wrote:

> 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_at_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_at_Vanderbilt.Edu
>>> ---------------------------------------------------------------------
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