[gmx-users] dihedral doubt

[Mark Abraham]

This is not needed, the code considers both ijkl and lkji order when
seeking a match.

Mark
On Mar 2, 2014 1:06 AM, "Andres Ortega Guerrero" <og_andres15 at hotmail.com>
wrote:

> Thanks Justin for your help, i will modify the i j k l of the dihedral in
> my topology to correspond to the bonded.itp
>
> Thanks again
>
>
> Andres Ortega
>
> > Date: Sat, 1 Mar 2014 18:39:04 -0500
> > From: jalemkul at vt.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] dihedral doubt
> >
> >
> >
> > On 3/1/14, 6:27 PM, Andres Ortega Guerrero wrote:
> > > Thanks Justin for the advice and help,
> > >
> > > So i have to add in the bonded.itp
> > > O_2 C_2 CT OH with the parameters?  or in the topology file (molecule)
> , y define the dihedral like OH CT C_2 O_2 ???
> > >
> >
> > Either way.  The dihedral's parameters either need to exist in any one
> of the
> > following:
> >
> > 1. In [dihedraltypes] in ffbonded.itp
> > 2. In the .top in a [dihedraltypes] directive declared before the first
> > [moleculetype]
> > 3. Explicitly printed on the line with the corresponding atom numbers in
> the
> > [dihedrals] directive
> >
> > If any of those is true, it will work.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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