[gmx-users] Re: RMSF error when fitting to average structure

Justin Lemkul jalemkul at vt.edu
Thu Aug 16 21:24:18 CEST 2012

On 8/16/12 3:19 PM, tdgrant1 wrote:
> Hi Justin,
> I did indeed correct for periodic boundary conditions prior to running rmsf,
> so I'm not sure what the problem would be there.

The message you got was a warning, not an error.  The warning is generic and is 
printed by any Gromacs program that does not receive a .tpr file passed to the 
-s flag.  It is not necessarily indicative of any problem but is written to be 
helpful to the user.

> Is there any way of producing an average structure from rmsf (or any other
> program for that matter) that is not output as a .pdb file but as a .tpr
> file?

You can easily produce a .tpr file from any coordinate file using an existing 
topology and .mdp file.  Coordinate files are not generally written in .tpr format.


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list