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

tdgrant1 tgrant at hwi.buffalo.edu
Thu Aug 16 16:13:27 CEST 2012

Dear all,

I have a 70 ns trajectory for which the last 60 ns appears to be
equilibrated.  I'm attempting to create a plot of RMSF but I want to align
it to the equilibrated structure, not the starting structure.  I first ran
g_rmsf using the starting structure as the reference structure over only the
last 60 ns and output the average structure (with B-factor column) using the
-ox flag.  I would now like to use this average, "equilibrium" structure as
the reference structure for fitting the entire trajectory.  

When I try and use this average structure as a reference structure with the
-s flag, I get the following error:

WARNING: if there are broken molecules in the trajectory file,
         they can not be made whole without a run input file 

I'm not sure if the "broken molecule" it's referring to is the average
structure, which I presume could be "broken" due to the unnatural bond
lengths and angles resulting from averaging or if there's a problem trying
to use a pdb file (which is the only -ox output file option) instead of a
.tpr file, which is the format of the original starting structure, which

Does anyone have a suggestion as to how to obtain this rmsf plot?

Thank you,

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