[gmx-users] Index group for Backbone/C-alpha of specific stretch of residues

[Navneet Kumar]

Thankyou!

On Fri, Jan 10, 2020 at 6:00 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/9/20 9:42 AM, Navneet Kumar wrote:
> > Thank You, sir!
> >
> > What If I want to extend the residues like choose c-alpha of 150-200 &
> > 60-70 in a single index group ?
>
> 3 & r 60-70 | 3 & r 150-200
>
> Type "help" at the make_ndx prompt for examples of how to use the program.
>
> -Justin
>
> >
> > On Wed, Jan 8, 2020 at 6:21 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 1/8/20 4:49 AM, Christian Blau wrote:
> >>> Hi Navnett,
> >>>
> >>>
> >>> gmx select will be your friend.
> >>>
> >>>
> >>> At the bottom of
> >>>
> >>>
> >>
> http://manual.gromacs.org/documentation/current/onlinehelp/selections.html
> >>>
> >>> you'll find some example commands. Something along the lines of
> >>>
> >>>    gmx select -select 'name CA and resid > 149 and resid < 211'
> >>>
> >>> should work.
> >>>
> >>>
> >>> It's a very powerful syntax and I figured for me it was very much
> >>> worth the effort reading through that documentation.
> >>>
> >> It's also simple in make_ndx:
> >>
> >> 3 & r 150-210
> >>
> >> Either way works. Whatever you find easier to use.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >> --
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> >
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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-- 






     Thanks & Regards
_______________________________________________________

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*NAVNEET KUMAR*
Doctoral Student
Dept. of Pharmacoinformatics
National Institute of Pharmaceutical Education and Research, Sector 67,
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