From: #YEO JINGJIE# (JYEO1_at_e.ntu.edu.sg)
Date: Fri Jan 06 2017 - 15:47:00 CST

Hi JC,

I noticed that in one of the Gaussian water interaction files, one hydrogen was visualised by VMD to be bonded to the diazosulfonic acid carbons. If I include all the Gaussian files for optimisation and following your advice to exclude atoms with low penalties, I would get some funky numbers:
C8 -0.950
N2 -0.971
C13 0.779
N3 1.142

However, even if I omit that anomalous Gaussian file, I get:
C8 -0.195
N2 0.402
C13 -0.592
N3 0.385

Any ideas what might have gone wrong?

Best,
JJ

On 6 Jan 2017, at 3:52 PM, JC Gumbart <gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu>> wrote:

You just doní»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.

Best,
JC

On Jan 6, 2017, at 1:52 PM, #YEO JINGJIE# <JYEO1_at_e.ntu.edu.sg<mailto: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

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,
Jingjie


**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.


**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.