onetwo wrote:
Hello Users,
I have a query regarding simulation with the ligand.
In my protein there are two ligands, one of them (coenzyme) is from the
crystal data, and other I have docked at the active site, while docking
it is showing good interaction with all the active site residues very
well.
I used GROMOS96 43a1 force field, and got the topology file made from
prodrg beta, using GROMOS 96.1 for both the ligands.
PRODRG produces notoriously bad topologies. See, for instance:
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
while doing equilibration I did, brendenson coupling on like
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
and in MD simulation also
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 300 300
There could be some debate about these settings, and I do not know the best way
to handle temperature coupling. It seems to me that if you have a ligand (or
multiple) bound to a protein, the interactions between the protein and ligand(s)
will be tightly coupled, such that you shouldn't lump the ligands into the
"Non-Protein" group, which in this case likely comprises solvent. Maybe someone
with more experience in these types of simulations can share some insight.
But after 1ns equibiration, one of the ligand (the one which I docked)
is going away from the active site and then I ran it for 4 ns further,
it has gone more far from the cavity. Following is the link to the
snapshot of the ligand at different time.
https://picasaweb.google.com/118389174994698260649/Md_complex?authkey=Gv1sRgCMis2qry3cGj7AE#5600499037480314402
I want to ask if the change in the
position of ligand is justified with the parameters i have taken or it
if i have done something wrong?
Without providing the actual topology(ies) of the ligand(s) and a complete .mdp
file, it is hard to say. But if you're using PRODRG output, I would suspect
that it would be the culprit.
-Justin
Thanks and Regards
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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