From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Mar 21 2016 - 08:19:53 CDT
Dear Farideh,
Have a look at the cgenff papers and tutorials (http://mackerell.umaryland.edu/~kenno/cgenff/) and the fftk documentation (http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/), which cover the approaches nicely.
Best,
Peter
> On Mar 21, 2016, at 8:31 AM, faride badalkhani <farideh.khamseh_at_gmail.com> wrote:
>
> Dear all,
>
> I have run my structure through CGenFF and got the parameters and charges. According to this file
>
> Penalties lower than 10 indicate the analogy is fair; penalties between 10 and 50 mean some basic validation is recommended; penalties higher than 50 indicate poor analogy and mandate extensive validation/optimization.
>
> The penalties in the .str file of my structure are not higher than 50, but there are some penalties between 10 and 50.
> Could you tell me what does basic validation mean? What kind of optimizations or calculations should I perform?
>
> Truly yours,
> Farideh
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