[gmx-users] Ligand during GPRC-membrane simulation
Justin A. Lemkul
jalemkul at vt.edu
Mon Oct 19 17:26:59 CEST 2009
Thielges, Sabine wrote:
> 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.
If your system is not behaving in the biologically-dictated manner, I would
guess that whatever parameters you are using are unsuitable. Which force field
are you using, and where did you get the ligand parameters? How were they
> 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.
You could implement distance restraints, but that would require merging the
moleculetypes, and again, if you're trying too hard to force something to
happen, I would seriously question the accuracy of what you're doing.
> 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.
Then you didn't actually apply position restraints. Did you use appropriate
"define" statements in the .mdp file (if necessary)?
> Could anyone help me?
> Thank you in advance
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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