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
--
========================================
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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