[gmx-users] Softcore potentail parameters help

Chris Shaw chrisbiochem at yahoo.co.uk
Thu Aug 19 10:54:32 CEST 2004

Hi Everyone, 
Can anyone give me some pointers regarding the paramaters used in softcore potentials. I have a ligand protein complex which i have generated with Autodock, and would like to refine it as the ligand is close to the proposed docking site not a little out. I have tried using MD to refine the initial dock (5ns), but the ligand stayed where is was. As i understand it softcore potential may allow a reduced potentail so that the ligand can overcome steric barriers etc? I really need some help on this

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