[gmx-users] Doubt in Distance Restraints

[raja]

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

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