[gmx-users] Doubt in Distance Restraints

[raja]

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

     
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  raja
  raja_28 at fastmail.us

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