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
validated?
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)?
-Justin
Could anyone help me?
Thank you in advance
Sabine
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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