Dear AMBER
Minimization of my complex (protein+inhibitor) seems to not working well.
I used LBFGS method for sander minimization. The initial energy of the complex is -5.78 and the final energy is -5.29 kcal.mol-1. why the final energy is higher than the initial energy?
On the other hand, I tested TNCG method, according to the manual, TNCG should give lower RMSD comparing to the initial structure. TNCG minimization in my case give me unrealistic results where it pushed the ligand away from the active site. Is there any explanation for this?
Cheers;
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Received on Wed Nov 02 2011 - 02:00:07 PDT
