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

[James Starlight]

and what the most trivial way to find correspondence of the line in
the data file to what I actually see on the its graph (projection)  ?
Sorry I'm not an expert of xmgrace so it might seems for you trivial
:)

Regards,

James

2015-04-17 20:18 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> --
> ==================================================
>
> 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.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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