[gmx-users] Doubt in Distance Restraints

[Tsjerk Wassenaar]

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
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