From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Jun 08 2012 - 21:10:04 CDT
as Axel suggested, decrease the time step. If you are doing energy
minimization first, make sure you have done enough steps to clear any bad
contacts (and if you aren't doing energy minimization first, maybe do that
first). If you are taking a minimized structure and just starting the
simulation at say 300K, try heating it slowly to 300K first.
You say the atom belongs to the ligand, can you try simulating the ligand
alone? It may be that something is wrong with your forcefield parameters,
and some atoms are being forced to a configuration that is far from your
input coordinates.
~Aron
On Fri, Jun 8, 2012 at 9:58 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Jun 8, 2012 at 9:23 PM, jose correa <corrjose_at_gmail.com> wrote:
> > Dear all
> > We are trying to achieve MD simulations on GPCR (in membrane) couple to
> > ligand, however, we have this error: ERROR: Constraint failure in RATTLE
> > algorithm for atom
> > The atom (one) that yield this error belong to ligand, do you have any
> > suggestions?.
>
> shorter time step?
>
> > Best wishes
> > José
> >
> > --
> > Ph.D. JOSE CORREA BASURTO. Professor of Medicinal Chemistry and molecular
> > modeling, Escuela Superior de Medicina, Instituto Politécnico Nacional,
> > México. Plan de San Luis Y diaz Mirón S/N, Col. Casco de Santo Tomas,
> Mexico
> > city, México. CP: 11340. Tel/Fax; (+5255) 57296000 Ext 62747 and 62767
> > e:mail: josecorreabasurto_at_hotmail.com or jcorreab_at_ipn.mx,
> corrjose_at_gmail.com
> > website: http://farmacologiacomputacional.blogspot.com/
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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