[gmx-users] Doubt in Distance Restraints
raja
raja_28 at fastmail.us
Thu Apr 20 06:15:37 CEST 2006
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
More information about the gromacs.org_gmx-users
mailing list