From: #YEO JINGJIE# (JYEO1_at_e.ntu.edu.sg)
Date: Thu Jan 12 2017 - 09:47:40 CST

Hi JC,

I've proceeded to the dihedral parameterisation but I encountered one dihedral which has not finished running in Gaussian even after two days. All other dihedral runs have finished (I had 14 jobs in total). May I know whether there is a way to check what went wrong and rectify it, or is this perfectly normal and I just have to restart and keep running?

Best,
JJ

On 9 Jan 2017, at 12:08 AM, JC Gumbart <gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu>> wrote:


Indeed, it is subjective but 1.0 sounds really good. There is no guarantee that subsequent rounds will monotonically improve.

Best,
JC

On Sun, Jan 8, 2017, 12:24 PM #YEO JINGJIE# <JYEO1_at_e.ntu.edu.sg<mailto:JYEO1_at_e.ntu.edu.sg>> wrote:
Thank you very much for the information, I will test that out and see how it goes.

I have another query regarding bond and angle fitting. I obtained an objective value close to 1.0 for the first downhill iteration, but subsequent iterations drove it up to approximately 3.0 and 9.0. Is this erroneous or is the first iteration already sufficient? Is a value close to 1.0 considered low (although I assume this would be rather subjective)?

Best,
JJ

On 7 Jan 2017, at 5:36 PM, JC Gumbart <gumbart_at_physics.gatech.edu<mailto:gumbart_at_physics.gatech.edu>> wrote:

C8 has a penalty of 0.00, why are you fitting it?

You need to balance atoms that are including with gaussian log files included. For example, if C8 is not being fit, doní»t include the gaussian file for its interaction with a water. Ultimately, it takes some trial and error with atoms and water-interaction data to include, along with multiple rounds of fitting, to figure out the right balance.

Best,
JC

On Jan 6, 2017, at 4:47 PM, #YEO JINGJIE# <JYEO1_at_e.ntu.edu.sg<mailto:JYEO1_at_e.ntu.edu.sg>> wrote:

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.


**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.