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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