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 <[EMAIL PROTECTED]> 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
[EMAIL PROTECTED]
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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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