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
inflated_system.tpr
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
understand.
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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