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

[Justin Lemkul]

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

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