On 4/28/2011 3:21 PM, 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.
while doing equilibration I did, brendenson coupling on like
; Berendsen temperature coupling is on in two groups
Tcoupl = V-rescale
You used V-rescale (per the command), not Berendsen (per the comment).
However, that's not a problem.
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
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?
It is well known (and published) that PRODRG can produce garbage
charges. Perhaps you have evidence of that here.
If you expect your ligand to stay bound, it may make more sense to
T-couple it with the protein, using a custom index group, then to couple
it with solvent. However, I'd look at my charges first.
Mark
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