AMBER Archive (2003)

Subject: Re: Running MD

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Mon Jun 23 2003 - 07:40:24 CDT

> AMBER ver is 6.0. The error has occured right at the begining of
> dynamics run.

at step 1? tell us the energies- are there high vdw energies?
is it solvated? is the pressure very high?

> There are no modified force fild parameters or non-standard
> molecules. It is protein taken from PDB and protonated with protonate
> program in AMBER.

how did you equilibrate it? was the energy minimized?

please, be specific or we cannot help.

>
> Balvinder
> > > ----- Original Message -----
> > From: "Balvinder Singh" <bvs_at_imtech.res.in>
> > To: "AMBER" <amber_at_heimdal.compchem.ucsf.edu>
> > Sent: Monday, June 23, 2003 1:33 PM
> > Subject: Running MD
> >
> >
> > >
> > > An error is occuring while running MD with SHAKE on. It is
> > >
> > > "RESETTING OF COORDINATES CAN NOT BE ACCOMPLISHED
> > > DEVIATION IS TOO LARGE
> > > ........."
> > >
> > > in mdout. Can anyone give clue how to overconme this?
> > >
> > > Balvinder
> > >
> > >
> >
> >
>
>