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From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Fri Jan 06 2017 - 14:52:50 CST
You just don’t even include those atoms with low penalties (< 10 at least, maybe higher) in the charge fitting. Their charges will be taken from the PSF file.
> On Jan 6, 2017, at 1:52 PM, #YEO JINGJIE# <JYEO1_at_e.ntu.edu.sg> wrote:
> Dear VMD users,
> I would like to use FFTK to determine the CHARMM parameters for diazonium-modified tyrosine. I am setting up the problem using a fragment approach, where I have the tyrosine residue and diazosulfonic-acid fragment. The .mol2 and .str files from paramchem are available here:
> https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=36055#Post36055 <https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=36055#Post36055>
> I've obtained the water interaction energies from Gaussian for the entire modified residue as well as only for the diazosulfonic-acid fragment alone. The question now is from which of this should I run the charge optimisations and which atoms ought to be constrained? From the paramchem results, the highest penalties are in the region around the -N=N- atoms. Should I then constrain the atoms such that only adjacent atoms are optimised, i.e., -C-N=N-C-?
> Best Regards,
> **Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University.