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

[Herbert de Castro Georg]

Thanks, Mahdi.

I'm aware of that study. Actually it's because of it that I have chosen the
latest CHARMM27 for the simulations.

Best,
Herbert

Em sáb., 4 de abr. de 2020 às 12:57, Mahdi Bagherpoor <mehdi.bpour at gmail.com>
escreveu:

> 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
> > >
> > > ==================================================
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.