VMD-L Mailing List

From: Lokendra Poudel (poudel_2039_at_tamu.edu)
Date: Wed Nov 18 2020 - 10:12:40 CST

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