Raja,
distance retraints are described in the manual (Section 4.3.4).
The potential form is given in Figure 4.13 (Gromacs 3.3 manual).
There you can find out what low (r0), up1 (r1) and up2 (r2) mean.
I also want to remind you that the distances are given in nanometers.
Hence the allowed unpenalized distance between atoms 3724 and 4734
as you defined it would be 20.9 angstroms, which probably not what
you want.
Best regards,
Uwe
raja 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
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