VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Wed Nov 18 2020 - 14:35:01 CST

Hi Lokendra,

I think we usually run SA first and then downhill. But it’s quite possible there is no unique solution. Instead, you likely have a very rugged energy landscape sprinkled with local minima that you are hopping between. This is going to be compounded if you have too many charges to optimize at once. So you’ll just have to decide what interactions are most important to get right (use COLP to help).

Best,
JC

On Nov 18, 2020, at 11:12 AM, Lokendra Poudel <poudel_2039_at_tamu.edu<mailto:poudel_2039_at_tamu.edu>> wrote:

Hi James,

I am trying to develop parameter and topology files for a hydrophobic ligand PDBu (76 atoms) using Force Field Toolkit (FFTK). I am in charge optimization step in fftk. The quantum mechanical calculations for water interaction sites run fine. After this, I tried to optimize the charge but the optimized charges are not converged .i.e charges are changing each iteration during optimization.
During optimization, I did the following steps
1/ in charge constraints: removed all non-polar Hydrogen and those atoms which have zero penalty score (CGENFF Program)
2/ in QM Target data: excluded those QM water interactions which clashing with other atoms and fly away from an atom.
3/ in advance setting: used simulated annealing with a different combinations such as
water shift setting +/-0.4, +/- 1.0, +/- 1.5, +/-2.0 and delta 0.05 or 0.1
optimize setting tolerance 0.005 0.001 0.01 distance weight 0.5/1.0 etc

After several attempts, my optimized charges are not converged. I spent almost more than two weeks on this but couldn't fix the problem. I would appreciate it if you could help me with it.

Thanks
Lokendra Poudel, PhD