[gmx-users] about how to create angle.index with specific angles

[Justin Lemkul]

On 4/29/20 7:11 PM, lazaro monteserin wrote:
> Dear Dr. Lemkul it could be possible use that angle.index with the selected
> dihedrals written by hand as index file for gmx angle for dihedral
> Principal Component Analysis?

You can create index groups however you like for whatever analysis you 
want to perform.

-Justin

>   Kindly,
> Lazaro
>
> On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 4/29/20 5:01 PM, lazaro monteserin wrote:
>>> Dear gromacs users,
>>>
>>> Is there any way to tell gmx mk_angndx to create the index file with
>>> dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g
>> 1,
>>> 2, 3) from my molecule?
>> mk_angndx is designed for distributions of similar angles (e.g.
>> evaluating force field sampling). If you want to compute specific
>> angles, use make_ndx or simply write the index groups by hand.
>>
>> -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

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