[gmx-users] Ligand during GPRC-membrane simulation

[Thielges, Sabine]

Hi everyone,

I am currently doing a simulation which involves a dopamine receptor
placed in a POPC membrane and an agonist or antagonist in the active
site. The ligand was placed by VS and is closed to what the biology
gives. My problem is that the ligand get out of is normal position
during the simulation. I know it is easier to move the ligand than the
receptor but that is not the biological answer. 
I would like to know if there is a way to fix the ligand so that the
receptor would be force to adapt around it and not the inverse. There is
know Hbonds with specific amino acid is it possible to add this
information in the run.

I tried so far to use position restraint in my ligand.itp

[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       10000      10000      10000
   3    1       10000      10000      10000
   4    1       10000      10000      10000
   5    1       10000      10000      10000
   6    1       10000      10000      10000
   8    1       10000      10000      10000
   9    1       10000      10000      10000
  10    1       10000      10000      10000
  11    1       10000      10000      10000
  12    1       10000      10000      10000
  13    1       10000      10000      10000

But it didn't have any effect on the final MD simulation of 10 ns. At
the end the ligand was completely out of the site.

Could anyone help me?

Thank you in advance 

Sabine