[gmx-users] Terminus Atoms genrestr?

[Justin A. Lemkul]

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" <jalemkul at 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
>  >
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> 
>  
> 
> TJ Mustard
> Email: mustardt at 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

========================================