[gmx-users] Extraction of the pdb data from the g_shame diagrams

[Justin Lemkul]

On 4/17/15 11:52 AM, James Starlight wrote:
> Dear Gromacs users!
>
> I'm looking for most trivial option to extract structural data from
> the free energy diagrams of PCA projections obtained by g_sham. E.g on
> the plots I've found transitions towards the relevant conformations
> along chosen PCs passed through several intermediates. How it's
> possible to extract pdb of the protein corresponded to those
> short-lived intermediates just form the projection data avoiding of
> the GUI visualization of the trajectory?
>

If you know what point you want (the line in the data file), that should be the 
frame number in the trajectory.  Then it's just a matter of trjconv -dump.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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