nitu sharma wrote:
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.
OK, but you still need to be seen to be applying your own
troubleshooting skills. If something doesn't work, try some
alternatives. :-)
Also, learn the lesson that if you don't have someone locally who is
useful to ask for basic help, don't take on the project!
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?
Position restraints aren't magic. If the other forces on your protein
are stronger then they'll overrule them. If they are very large, then
you have a serious problem with your structure, or your model physics
(i.e. the contents of your .itp files). To find out where the problem is
coming from, you need to simplify your problem. Remove an element and
see how things work differently. So try not using inflategro.pl, or
changing its settings, or not using both your proteins, or not using any
proteins, or not using position restraints.
I don't think you've ever mentioned where you got the contents of your
.itp files from. If your structure after inflategro.pl is fine, and it's
not after you apply some physics to it, then your physics is broken. We
can't help more than that without a lot more information.
Mark
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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