Justin,
Ok, if I find a way I will post it back here. And thank you for the recommendations.
Thank you,
TJ Mustard
On February 11, 2011 at 11:05 AM "Justin A. Lemkul" <jalem...@vt.edu> wrote:
>
>
> TJ Mustard wrote:
> >
> >
> > Justin,
> >
> >
> > Yes but how can I automatically select the terminal residue's alpha
> > carbons, without having to individually select residues?
> >
> >
> >
> > 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.
> >
> >
>
> I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough to
> determine terminal residues on its own. If you have multiple copies of the same
> molecule, then you know how many atoms are in each, so you can script a little
> loop that will do it for you, otherwise I don't think there's anything that will
> do this job on its own. Maybe g_select, but its capabilities and syntax are not
> yet well-documented.
>
> -Justin
>
> >
> >
> >
> > Thank you,
> >
> > TJ Mustard
> >
> > On February 11, 2011 at 10:30 AM "Justin A. Lemkul" <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > TJ Mustard wrote:
> > > >
> > > >
> > > > Hi all,
> > > >
> > > >
> > > > Does anyone know how to make a positional restraint file for the
> > > > terminal atoms in a protein/rna/dna chain via genrestr? I know I
> > can get
> > > > the backbone, C-alpha, etc.
> > > >
> > > >
> > > >
> > > > Doing this by hand will be time consuming, and if there was an
> > automated
> > > > way of doing this I would be very happy.
> > > >
> > > >
> > >
> > > Like the other Gromacs utilities, genrestr can make use of index files.
> > >
> > > -Justin
> > >
> > > >
> > > >
> > > > Thank you,
> > > >
> > > > TJ Mustard
> > > >
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > --
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> >
> >
> >
> > TJ Mustard
> > Email: musta...@onid.orst.edu
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
> TJ Mustard wrote:
> >
> >
> > Justin,
> >
> >
> > Yes but how can I automatically select the terminal residue's alpha
> > carbons, without having to individually select residues?
> >
> >
> >
> > 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.
> >
> >
>
> I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough to
> determine terminal residues on its own. If you have multiple copies of the same
> molecule, then you know how many atoms are in each, so you can script a little
> loop that will do it for you, otherwise I don't think there's anything that will
> do this job on its own. Maybe g_select, but its capabilities and syntax are not
> yet well-documented.
>
> -Justin
>
> >
> >
> >
> > Thank you,
> >
> > TJ Mustard
> >
> > On February 11, 2011 at 10:30 AM "Justin A. Lemkul" <jalem...@vt.edu> wrote:
> >
> > >
> > >
> > > TJ Mustard wrote:
> > > >
> > > >
> > > > Hi all,
> > > >
> > > >
> > > > Does anyone know how to make a positional restraint file for the
> > > > terminal atoms in a protein/rna/dna chain via genrestr? I know I
> > can get
> > > > the backbone, C-alpha, etc.
> > > >
> > > >
> > > >
> > > > Doing this by hand will be time consuming, and if there was an
> > automated
> > > > way of doing this I would be very happy.
> > > >
> > > >
> > >
> > > Like the other Gromacs utilities, genrestr can make use of index files.
> > >
> > > -Justin
> > >
> > > >
> > > >
> > > > Thank you,
> > > >
> > > > TJ Mustard
> > > >
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Ph.D. Candidate
> > > ICTAS Doctoral Scholar
> > > MILES-IGERT Trainee
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > --
> > > gmx-users mailing list gmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> >
> >
> >
> > TJ Mustard
> > Email: musta...@onid.orst.edu
> >
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
TJ Mustard
Email: musta...@onid.orst.edu
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
