VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Oct 16 2015 - 02:50:39 CDT

Bryan,

Apologies for a delayed response; I have been traveling internationally.

Yes, it is generally a good idea to include enough of the known atoms to cover the connection between known and unknown parameters. ffTK is designed so that it is easy to optimize a subset of parameters — in this case, retain the known parameters and optimize only the missing ones.

For the specific case of charges, the typical method used is:
1) Set any “known” charges in the PSF file.
2) When setting the Charge Constraints (Opt. Charges -> Charge Constraints -> Charge Group) simply remove the known atoms from the constraints box.
—> This process will optimize any atoms contained within the charge constraints while fixing the charge on the atoms that are not included in the box.

When analyzing the optimization output, the raw objective function is not particularly informative. The COLP tool (available from Opt. Charges -> Results -> Open COLP) allows users to deconvolute the objective function and inspect each of the contributing terms. This allows you to judge which terms contribute the most to the objective function, and to identify problematic atoms.

Regards,
Christopher Mayne


On Oct 13, 2015, at 9:08 PM, Bryan Roessler <roessler_at_uab.edu<mailto:roessler_at_uab.edu>> wrote:

Hello,

When parameterizing novel molecular fragments that will eventually be bonded to a residue with an existing forcefield, it is necessary to incorporate some of the atoms near the bond from the residue with existing forcefields that contribute to the dihedral, angle and bond parameters in the QM/MM optimization scheme.

Is it then suggested that when performing the charge optimization step in fftk, I maintain the charges on those overlapping atoms as they exist in the CHARMM ffs as best as possible? In other words, should I create an upper and lower bound (so that the optimizer still has some 'play') that are very near the charge values on those atoms provided in the existing forcefield? Or should I let all of the charges optimize independently of the existing forcefield charge parameters?

When I allow all of the charges to optimize without strict bounding, I can attain a total objective that is very near zero after several iterative optimization passes. However, when I loosely 'fix' the charges of some of the overlapping atoms that already exist in the forcefield, the charge optimization objective values are not nearly as good (which is to be expected as the degrees of freedom are reduced). However, in some cases the charges on the overlapping atoms can be quite different than the existing charge values in the the CHARMM ff if I let them optimize without restraints.

Thanks for your help in advance,

Bryan

Bryan Roessler | Graduate Research Assistant
UAB | The University of Alabama at Birmingham
uab.edu/cmdb<https://urldefense.proofpoint.com/v2/url?u=http-3A__uab.edu_cmdb&d=BQMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=KWvVUHl42S-_kpj6OunU5-512j104OJKVMt2MxKKoE8&m=UR25lRZr0C3xV-q365GEQC5DLXFQ-9OHyfrhlmz9W_I&s=Suif7QoxGTUSvDyHPNpdlgb6hRzZkYZtDAvfvXiSfjQ&e=>
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