[gmx-users] Aromatic rings not plane after minimization

[Pierre THEVENET]

I am not using any rtp file. I thought the default parameters would be ok
for standard amino acids.
As I tried with different gromos force field, I suppose that I need to use
a rtp file. But I don't understand
what must be written in this file.

--------------------------

Pierre THEVENET
Ph.D. Student
INSERM - MTi
Ecole Doctorale B3MI
Université Paris Diderot - Paris 7

2014-04-15 16:25 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Only if the .rtp has them for the force field you are actually using...
>
> Mark
>
>
> On Tue, Apr 15, 2014 at 4:03 PM, Pierre THEVENET <pithevenet at free.fr>
> wrote:
>
> > >
> > > I do not know how you do the magic connected with the topology
> > > derivation, but please make sure that all needed dihedrals were
> > > introduced. x2top, for instance, does not write dihedrals.
> > >
> > >
> > To produce the topology, I use pdb2gmx, I thought it would write the
> proper
> > dihedrals. Am I wrong?
> >
> > Thanks for your help.
> > --
> > 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.
>