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<p style="margin: 0px;">Justin,</p>
<p style="margin: 0px;"><span><br />
</span></p>
<p style="margin: 0px;"><span>Yes but how can I automatically select the terminal residue's alpha carbons, without having to individually select residues?</span></p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;">Read the manual and some internet pages and found that you can easily select the alpha carbons on select residues by specifying them with the argument r_#_#_#_#_#_#... etc in make_ndx, which can then be used to make a positional restrain file via makerestr. I am just hoping there is a better, more automated way of doing this.</p>
<p style="margin: 0px;"> </p>
<p style="margin: 0px;"><span> </span></p>
<p style="margin: 0px;"><span>Thank you,</span></p>
<p style="margin: 0px;"><span>TJ Mustard<br />
</span></p>
<div style="margin: 5px 0px 5px 0px;">
On February 11, 2011 at 10:30 AM "Justin A. Lemkul" <jalemkul@vt.edu> wrote:<br />
<br />
><br />
><br />
> TJ Mustard wrote:<br />
> ><br />
> ><br />
> > Hi all,<br />
> ><br />
> ><br />
> > Does anyone know how to make a positional restraint file for the<br />
> > terminal atoms in a protein/rna/dna chain via genrestr? I know I can get<br />
> > the backbone, C-alpha, etc.<br />
> ><br />
> > <br />
> ><br />
> > Doing this by hand will be time consuming, and if there was an automated<br />
> > way of doing this I would be very happy.<br />
> ><br />
> ><br />
><br />
> Like the other Gromacs utilities, genrestr can make use of index files.<br />
><br />
> -Justin<br />
><br />
> > <br />
> ><br />
> > Thank you,<br />
> ><br />
> > TJ Mustard<br />
> ><br />
><br />
> --<br />
> ========================================<br />
><br />
> Justin A. Lemkul<br />
> Ph.D. Candidate<br />
> ICTAS Doctoral Scholar<br />
> MILES-IGERT Trainee<br />
> Department of Biochemistry<br />
> Virginia Tech<br />
> Blacksburg, VA<br />
> jalemkul[at]vt.edu | (540) 231-9080<br />
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br />
><br />
> ========================================<br />
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</div>
<p style="margin: 0px;"> </p>
<p style="font-family: monospace; white-space: nowrap; margin: 5px 0px 5px 0px;">TJ Mustard<br />
Email: mustardt@onid.orst.edu</p>
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