[gmx-users] Generation of the Distance Restraints

[James Starlight]

Mark, Justin,

Thanks for advises. Indeed I think that simple text editor would be better
sollution in my casw because of small number of restraints.

I just have a question about definition of the Distances

This is the default of the restraints between atom 10 and 16.

[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
  10 16 1    0     1     0.0 0.3 0.4 1.0



I'd like to restrict distance between both of that atoms   7.96 < r(Ca-Ca)<
8.41

I've found that the up1 is the 7.96 and up2 is the 8.41 but how I could
specify 'low' in the above table ? Should I obtain value for the initial
Ca-Ca distance between my residues from the initial structure? How I could
do it?


James






12 марта 2012 г. 18:38 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:

>
>
> James Starlight wrote:
>
>> Francesca,
>>
>> Yes I suppose this is good aproach for the generation of position
>> restricktions on the desired atoms. But I want to restrain the distance
>> between selected pairs of atoms ( e.g between C-alpha- C-alpha atoms of two
>> different residues).
>>
>>
> How many restraints do you need to create?  If they are this simple, you
> can write them yourself using a text editor in conjunction with manual
> section 4.3.4.  Using genrestr is only really helpful when you require a
> network of distance restraints between the atoms of a given group.  If
> there are only a few to create, it's actually more work to use make_ndx and
> genrestr than it is to fire up your favorite text editor.
>
>
>  Also I want to restrain some dihedral angles in the desired rotameric
>> forms.
>>
>>
> See manual section 4.3.3 and http://www.gromacs.org/**
> Documentation/How-tos/**Dihedral_Restraints<http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints>
> .
>
>
>  In literature I've found that peple have dome the same things in Gromacs
>> but I could not find detailed algorithm of such methodology :(
>>
>>
> All relevant equations are provided in the manual, and examples are
> provided either there or on the Gromacs site.  If you need further
> information, ask a specific question related to what you can't find or
> don't understand.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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