[gmx-users] Generation of the Distance Restraints
jmsstarlight at gmail.com
Tue Mar 13 08:12:05 CET 2012
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)<
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
12 марта 2012 г. 18:38 пользователь Justin A. Lemkul <jalemkul at vt.edu>написал:
> James Starlight wrote:
>> 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
> See manual section 4.3.3 and http://www.gromacs.org/**
> 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 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
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