[gmx-users] CGENFF validation / optimization

[Justin Lemkul]

On 2/18/20 2:28 PM, Adarsh V. K. wrote:
> Dear all,
>
> While suing CGENFF server for " *.str " file generation, Few of the
> penalties were found to be higher than 50. How to do
> validation/optimization.? Is there any recommended softwares / servers
> available for

I suggest you read the 2010 JCC paper on CGenFF, which is itself a case 
study/tutorial on what to do. Other subsequent papers explain what the 
penalties mean and how to interpret them.

-Justin

> * " extensive validation / optimization." or any standard procedure
> available to do validation / optimization ?The *.str file also contains the
> following message.*
> ------------------------------------------------------------------------------------------------------------
> ! "penalty" is the highest penalty score of the associated parameters.
> ! 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.
> -------------------------------------------------------------------------------------------------------------

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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