[gmx-users] How to parametrize a new molecule?

[Mahdi Bagherpoor]

Hello Herbert,

Not related to your question, but be careful if you are going to use
CHARMM36 force field for DNA, as a recent study (
https://pubs.acs.org/doi/10.1021/acs.jpcb.9b09106) shows that this ff does
not preserve DNA stability at a longer time scale, in case you are going to
do so.

Best,
Mahdi

On Sat, Apr 4, 2020 at 3:21 AM Herbert de Castro Georg <hcgeorg at ufg.br>
wrote:

> Thanks, Justin!
>
>
>
> Em sex., 3 de abr. de 2020 às 22:15, Justin Lemkul <jalemkul at vt.edu>
> escreveu:
>
> >
> >
> > On 4/3/20 9:12 PM, Herbert de Castro Georg wrote:
> > > Dear users,
> > >
> > > I want to perform a simulation of a molecule inside DNA. I'm probably
> > going
> > > to use CHARMM for DNA. But how do I parametrize the molecule?
> >
> > http://cgenff.umaryland.edu/
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > 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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