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

[Mark Abraham]

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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> 
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