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<p style="margin: 0px;"><span>Justin,</span></p>
<p style="margin: 0px;"><span> </span></p>
<p style="margin: 0px;"><span>Ok, if I find a way I will post it back here. And thank you for the recommendations.<br />
</span></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>
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On February 11, 2011 at 11:05 AM "Justin A. Lemkul" <jalemkul@vt.edu> wrote:<br />
<br />
><br />
><br />
> TJ Mustard wrote:<br />
> ><br />
> ><br />
> > Justin,<br />
> ><br />
> ><br />
> > Yes but how can I automatically select the terminal residue's alpha<br />
> > carbons, without having to individually select residues?<br />
> ><br />
> > <br />
> ><br />
> > Read the manual and some internet pages and found that you can easily<br />
> > select the alpha carbons on select residues by specifying them with the<br />
> > argument r_#_#_#_#_#_#... etc in make_ndx, which can then be used to<br />
> > make a positional restrain file via makerestr. I am just hoping there is<br />
> > a better, more automated way of doing this.<br />
> ><br />
> > <br />
><br />
> I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough to<br />
> determine terminal residues on its own.  If you have multiple copies of the same<br />
> molecule, then you know how many atoms are in each, so you can script a little<br />
> loop that will do it for you, otherwise I don't think there's anything that will<br />
> do this job on its own.  Maybe g_select, but its capabilities and syntax are not<br />
> yet well-documented.<br />
><br />
> -Justin<br />
><br />
> ><br />
> > <br />
> ><br />
> > Thank you,<br />
> ><br />
> > TJ Mustard<br />
> ><br />
> > 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<br />
> > 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<br />
> > 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 />
> >  > --<br />
> >  > gmx-users mailing list    gmx-users@gromacs.org<br />
> >  > http://lists.gromacs.org/mailman/listinfo/gmx-users<br />
> >  > Please search the archive at<br />
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br />
> >  > Please don't post (un)subscribe requests to the list. Use the<br />
> >  > www interface or send it to gmx-users-request@gromacs.org.<br />
> >  > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br />
> >  ><br />
> ><br />
> > <br />
> ><br />
> > TJ Mustard<br />
> > Email: mustardt@onid.orst.edu<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 />
> --<br />
> gmx-users mailing list    gmx-users@gromacs.org<br />
> http://lists.gromacs.org/mailman/listinfo/gmx-users<br />
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br />
> Please don't post (un)subscribe requests to the list. Use the<br />
> www interface or send it to gmx-users-request@gromacs.org.<br />
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br />
>
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<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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