[gmx-users] Problem in applying postion restrain on protein

nitu sharma sharmanitu35 at gmail.com
Thu Apr 30 08:34:11 CEST 2009

Hello Justin sir

        sorry , The suggestion U given to me is not working. Actually I am a
master student and just started to do simulation of membrane protein . Here
no one did this work thats why i am facing more problem. sorry for putting
question all the time in gmx-user list . But its only option for me to
getting some information about my work.

Now, The the is still there . The main problem at this time is after
inserting protein prorein into lipid bilayer by using inflategro script-

./inflategro.pl system.gro 4 DMP 14 inflated_system.gro 5 inflated_area.dat
this works and the structure I have got from here looks fine , in next step
I am doing enegy minimisation of  inflate_system.gro by using grompp-
grompp -f em.mdp  -c Inflated_system.gro -p topol.top  -o
with mdrun- mdrun -v -s inflated_system.tpr -o inflated_system.trr -c
inflated-em.pdb -e inflated-em.edr -g inflated-em.log
This works  well  for 1000 nstep but structure I am getting from here the
protein is totally distorted why?
Even after applying strong position restrsain on protein.
The em.mdp file is-

pp                 =  /usr/bin/cpp
define              =  -DPOSRES
constraints         =  none
integrator          =  steep
nsteps              =  1000
;       Energy minimizing stuff
emtol               =  1000
emstep              =  0.0001

nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no
comm-mode           = Linear
pbc                 = XYZ

Is anything wrong in applying postion restrain in parameter file?

this is topology file-
; Include forcefield parameters
#include "ffG53a6_lipid.itp"

; Include chain topology
#include "topol_A.itp"
#include "topol_B.itp"

; Include DMPC chain topology
#include "dmpc.itp"

[ system ]
; Name
Protein in DMPC bilayer

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_B           1
DMPC               120

Where I should make changes to make protein as rigid molecule I am unable to

can u suggest me something ? I am asking again becoz the step of compression
and minimisation is working but the protein structure become distorted , and
I want to keep protein in its proper configuration.
Any suggestion specific to this will really helpful for me.

Nitu sharma
School of Life Sciences
Jawaherlal nehru University
New Delhi,India
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