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

[Justin Lemkul]

On 8/16/12 10:13 AM, tdgrant1 wrote:
> 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
> worked.
>
> Does anyone have a suggestion as to how to obtain this rmsf plot?
>

The warning about broken molecules relates to the trajectory (as stated in the 
message), so periodicity effects are not accounted for if you are not using a 
.tpr file.  Thus you could get erroneous results unless you have already 
corrected for PBC effects using trjconv before running g_rmsf.

-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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