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

[Justin Lemkul]

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
-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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