[gmx-users] Re: RMSF error when fitting to average structure
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
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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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