Re: AMBER: error due to exceeding left-hand side digital numbers in restart output

From: David A. Case <>
Date: Mon, 18 Jun 2007 11:06:16 -0700

On Mon, Jun 18, 2007, Cenk Andac wrote:
> I have been running a 300 ns MD for an RNA hairpin solvated by TIP3
> waters. somewhere around 50 ns of MD , I seem to get some errors with
> restart files so that the next sander routine does not start. After
> going through the coordinates in the previous restart file, I have
> noticed that some coordinates were filled with lots of stars, like
> ****.******* , instead of numbers.

There is not much you can really do here. Back up to the last good restart
file, and start again, setting iwrap=1 in the sander input. Going to netcdf
trajectory output would also eliminate this problem, but I think most people
(including me!) have been slow to make the change to the new format.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Jun 20 2007 - 06:07:24 PDT
Custom Search