AMBER Archive (2003)

Subject: Re: Running MD

From: Balvinder Singh (bvs_at_imtech.res.in)
Date: Mon Jun 23 2003 - 13:02:33 CDT

AMBER ver is 6.0. The error has occured right at the begining of
dynamics run. There are no modified force fild parameters or non-standard
molecules. It is protein taken from PDB and protonated with protonate
program in AMBER.

Balvinder

On Mon, 23 Jun 2003, Carlos Simmerling wrote:

> how you deal with the problem depends on when
> it happened. please give more details:
>
> what amber version
> when the error occurred
> do you have any modified force field parameters or
> non-standard molecules
> your equilibration procedure
>
> send these to the amber list.
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Assistant Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
>
> ----- 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
> >
> >
>
>