Hi! I would to design new small molecule based on the co-crystal of target protein and ligand using MOE software. Part of ligand will be maintained and I will modify the other part. The other part of new built molecule is not always at lowest energy. If click “minimize", the whole small molecule and the target protein will change conformation. Would you provide any suggestion? Thank you!
Dear Xu,
For energy minimization of selected part of ligand's atoms, you have to press shift key of your keyboard and select the atoms which you want to minimize. After selection go to the compute tab of MOE and choose energy minimization tab.
Now click on select atoms only option in energy minimization tab and change the gradient to 1.0 and press ok, this will minimize the only your selected part of the ligands. Repeat the same with the gradient from 1.0 to 0.00001.
Hope this will work and solve your problem.
In addition you may also save your ligand file separately from the MOE, since it will not change ligand coordinates and you can do the same process as mentioned above for ligand only. Now you can import the same energy minimized ligand into your receptor. This will also provide you the same result.
Regards Varun
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