[gmx-users] Doubt in Distance Restraints

[Tsjerk Wassenaar]

Hi Raja,

Yes, that's the idea. So funct (which is 2 now) is changed to 6, but you
will still need to specify the equilibrium bond length and the force
constant. The bond length can be chosen from the crystal structure, if no
other information is available, and the force constant isn't too important
if the purpose is too keep the things together. But there must be some
parameters for Fe(II)-ligand bonds lying around somewhere.

Cheers,

Tsjerk

On 4/25/06, raja <raja_28 at fastmail.us> wrote:
>
> Hi Mr.Tsjerk,
>         Thanks for your reply and I checked manual based on your
>         suggestion. I just want to make it sure, Is it what the manual
>         says while adding type 6 bond that is  to edit the protein.top
>         file under [bond] section so as to depict harmonic interaction
>         between metal and ligating atoms.
>
> ###################################
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2
> c3
> 4734  3724    2
> 4734  2839    2
> 4734  2872    2
> #####################################
>
> Where 4734 is Fe(II) atom and 3724,2839,2872 are respective metal
> chelating atoms of protein.
>
> Is it ok ?
>
> With thanks !
> B.Nataraj
>
>
>
> On Thu, 20 Apr 2006 10:11:34 +0200, "Tsjerk Wassenaar"
> <tsjerkw at gmail.com> said:
> > Hi Raja,
> >
> > You may be better off just adding bonds. I believe there was a bond type
> > (type 6) which was especially useful (intended?) for keeping metals
> bound
> > to
> > a protein.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On 4/20/06, raja <raja_28 at fastmail.us> wrote:
> > >
> > > Dear all,
> > >       My intention is to restrict Fe(II) in active site by distance
> > >       restraint protocol. Fe(II) is ligated by three amino acides'
> polar
> > >       atoms respectively by (1) NE2 of HIS ,(2) NE2 of HIS (3) OD1 of
> > >       ASP. The following is the disres itp file I used (copied from
> > >       manual3.3). where I edited the atom number of
> > >       aminoacids(3724,2839,2872) and Fe(II) as 4734.
> > > ############################# disres.itp
> > >
> > >
> #############################################################################
> > > [ distance restraints ]
> > > ; ai   aj    type    index    type'     low   up1   up2   fac
> > > 3724  4734   1        0        1        0.0  2.09  0.4   1.0
> > > 2839  4734   1        0        1        0.0  2.25  0.4   1.0
> > > 2872  4734   1        0        1        0.0  2.18  0.4   1.0
> > >
> > >
> > >
> ########################################################################################################################
> > >
> > > I do not understand the meaning of up2 and fac so I left with 0.4  and
> > > 1.0 as such as found in manual.
> > >
> > > In mdp file I added the following the commands
> > >
> > > ###################### full.mdp
> > >
> > >
> ######################################################################################
> > >
> > > define                   = -DDISRES
> > > disre                    = Simple
> > >
> > >
> #######################################################################################################################
> > >
> > > I expected these modifictions will restrict but those distances are
> not
> > > restrainted....why ?
> > >
> > > Kindly explain me that wheather I need to change any other parameter .
> > >
> > > With thanks !
> > > B.Nataraj
> > >
> > >
> > > --
> > >   raja
> > >   raja_28 at fastmail.us
> > >
> > > --
> > > http://www.fastmail.fm - IMAP accessible web-mail
> > >
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> >
> >
> >
> > --
> >
> > Tsjerk A. Wassenaar, M.Sc.
> > Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> > Dept. of Biophysical Chemistry
> > University of Groningen
> > Nijenborgh 4
> > 9747AG Groningen, The Netherlands
> > +31 50 363 4336
> --
>   raja
>   raja_28 at fastmail.us
>
> --
> http://www.fastmail.fm - I mean, what is it about a decent email service?
>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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