From: Mayne, Christopher G (
Date: Tue Jun 20 2017 - 09:12:15 CDT


Please continue to cc VMD-L so that others can learn from our conversation.

If you’ve already done everything else in ffTK, why wouldn’t you continue in ffTK and refine that dihedrals? I only provided other tools as (potential) alternatives, but ffTK is very good at optimizing dihedrals.

Christopher Mayne

On Jun 20, 2017, at 12:11 AM, saeed amini <<>> wrote:

Dear Christopher

Thanks a lot. Unfortunately I have optimized the rest of parameters for my molecule including charges, angles and ... by fftk. Can I optimize parameters by two different tools?

Best Regards

On Mon, Jun 19, 2017 at 7:49 PM, Mayne, Christopher G <<>> wrote:
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:
The MacKerell lab has released a dihedral fitting tool:
Pande’s lab (now L-P Wang) develops force balance:

Christopher Mayne

On Jun 18, 2017, at 7:37 AM, saeed amini <<>> 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