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 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? Thanks and Regards
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