Re: Topology and parameter files for flavonoid compounds

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jan 24 2020 - 06:08:20 CST

If you are using the CHARMM force field, look for documentation here:
http://cgenff.maryland.edu/
or alternatively, if you are using the AMBER force field, look here:
http://ambermd.org/antechamber/gaff.html

For a CHARMM-based force field, a useful tool is the VMD plugin called
"fftk":
http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/

The documentation in each page should be well enough get you started.

Giacomo

On Fri, Jan 24, 2020 at 1:49 AM Shruthi M (116011752017) Res/Bio-Tech <
shruthim_at_pmu.edu> wrote:

> Hi
> Please someone let me know how to generate topology and parameter files
> for a flavonoid compound to perform simulations in NAMD.
> Thanks in advance.
> Shruthi
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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