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.
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
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>
>
>
> 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
-- 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
