VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Jun 19 2017 - 10:19:54 CDT

Hi Saeed,

If the CGenFF web server returned high penalties, they suggest that you at least validate or refine them. I would suggest that you do this in ffTK, but I wrote the program, so I’m a little biased. There are other tools around that you could look into:

Benoit Roux’s lab runs the GAAMP web server: http://gaamp.lcrc.anl.gov/
The MacKerell lab has released a dihedral fitting tool: http://mackerell.umaryland.edu/ff_dev.shtml#dihfit
Pande’s lab (now L-P Wang) develops force balance: http://www.lpwchem.org/code-data/

Regards,
Christopher Mayne

On Jun 18, 2017, at 7:37 AM, saeed amini <aminisaeed1_at_gmail.com<mailto:aminisaeed1_at_gmail.com>> wrote:

Hi Everyone

As I understood, fftk propose to obtain dihedral parameters including nonpolar hydrogen atoms of our own molecule by available data in cgenff. Unfortunately, neither cgenff support my dihedral angle including nonpolar hydrogen atoms nor paramchem provides data with acceptable penalty {penalties are about 50}. Hereby I would like to inform me that either should I optimize them in fftk or there is another way to obtain them. any suggestion is appreciated.


Best Regards