[gmx-users] MD on protein-RNA complex

[Johnny Lu]

I guess:
multi-chain means the system has multiple chains of polymer (such as
peptide, or DNA/RNA). Some proteins have several peptide chains connected
together.
heterogeneous system: protein and RNA are different, and so protein + RNA
is a heterogeneous system.

Gromacs can simulate protein + RNA + water well, if the force field used
can accurately describe the three components and the interaction between
them.
I don't know how accurate is the force-field that you use, in describing
your system.

In a perfect world, we have a force field that can accurately describe
everything. Then, we can nearly simulate everything accurately.

On Fri, Mar 6, 2015 at 4:16 AM, Brett <brettliu123 at 163.com> wrote:

> Dear Justin,
>
> What do you mean for "Multi-chain and heterogeneous systems work out of
> the box"?
>
> I am looking forward to getting your reply.
>
> Brett
>
>
>
>
>
> At 2015-03-04 10:50:10, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> >
> >
> >On 3/3/15 9:34 PM, Brett wrote:
> >> Dear Justin,
> >>
> >>
> >> I mean is any difficulty or special for gromacs to recognize the RNA in
> the PDB file?
> >>
> >
> >Multi-chain and heterogeneous systems work out of the box.  As with
> anything,
> >the force field has to support everything and the nomenclature has to
> match the
> >force field's expectations, but pdb2gmx will take care of everything.
> >
> >-Justin
> >
> >--
> >==================================================
> >
> >Justin A. Lemkul, Ph.D.
> >Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> >Department of Pharmaceutical Sciences
> >School of Pharmacy
> >Health Sciences Facility II, Room 629
> >University of Maryland, Baltimore
> >20 Penn St.
> >Baltimore, MD 21201
> >
> >jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >http://mackerell.umaryland.edu/~jalemkul
> >
> >==================================================
> >--
> >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.
>