Hello Justin sir<br><br> 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.<br>
<br>Now, The the is still there . The main problem at this time is after inserting protein prorein into lipid bilayer by using inflategro script-<br><br>./inflategro.pl system.gro 4 DMP 14 inflated_system.gro 5 inflated_area.dat<br>
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-<br>grompp -f em.mdp -c Inflated_system.gro -p topol.top -o inflated_system.tpr<br>
with mdrun- mdrun -v -s inflated_system.tpr -o inflated_system.trr -c inflated-em.pdb -e inflated-em.edr -g inflated-em.log<br>This works well for 1000 nstep but structure I am getting from here the protein is totally distorted why? <br>
Even after applying strong position restrsain on protein.<br>The em.mdp file is-<br><br>pp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = none<br>integrator = steep<br>
nsteps = 1000<br>;<br>; Energy minimizing stuff<br>;<br>emtol = 1000<br>emstep = 0.0001<br><br>nstcomm = 1<br>ns_type = grid<br>rlist = 1<br>
rcoulomb = 1.0<br>rvdw = 1.0<br>Tcoupl = no<br>Pcoupl = no<br>gen_vel = no<br>comm-mode = Linear<br>pbc = XYZ<br><br>Is anything wrong in applying postion restrain in parameter file?<br>
<br>this is topology file-<br>; Include forcefield parameters<br>#include "ffG53a6_lipid.itp"<br><br>; Include chain topology<br>#include "topol_A.itp"<br>#include "topol_B.itp"<br><br>; Include DMPC chain topology<br>
#include "dmpc.itp"<br><br>[ system ]<br>; Name<br>Protein in DMPC bilayer<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>Protein_B 1<br>DMPC 120<br><br>Where I should make changes to make protein as rigid molecule I am unable to understand.<br>
<br>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.<br>Any suggestion specific to this will really helpful for me.<br>
<br>Nitu sharma <br>School of Life Sciences<br>Jawaherlal nehru University<br>New Delhi,India<br>