[gmx-users] Index file regarding

[Justin Lemkul]

On 5/7/18 9:31 AM, RAHUL SURESH wrote:
> Hi, I have created the index file. Now I want to calculate the rmsd of the
> C-alpha atoms of the index group alone.. So what group should i select?

Please state your goals directly rather than leaving details to come out 
bit by bit, it's much more efficient for you to get the resolution you 
need in fewer emails.

You can get examples of how to use make_ndx if you type "help" at its 
prompt.

You can create a merged group of CA atoms and your custom group of 
residues in basically the same way. If you've already created the group 
of discontinuous residues (replace X with the actual group number in the 
existing index file):

X & a CA

-Justin

> On Mon, May 7, 2018 at 6:50 PM, RAHUL SURESH <drrahulsuresh at gmail.com>
> wrote:
>
>> thank you.
>>
>> On Mon, May 7, 2018 at 3:39 PM, Shreyas Kaptan <shreyaskaptan at gmail.com>
>> wrote:
>>
>>> It's 'r37-70 | r 120-167 | ...'  so on and so forth.
>>>
>>> On Mon, May 7, 2018 at 12:06 PM RAHUL SURESH <drrahulsuresh at gmail.com>
>>> wrote:
>>>
>>>> Dear all,
>>>>
>>>> My protein structure has 400 residues of which I want to calculate RMSD
>>> of
>>>> particular 200 residues (approx) and they are not continuous. For
>>> example,
>>>> from 34-70; 120-167; 180-210;.... For this how can I create an index
>>> file?
>>>> Thank you
>>>>
>>>> --
>>>> *Regards,*
>>>> *Rahul Suresh*
>>>> *Research Scholar*
>>>> *Bharathiar University*
>>>> *Coimbatore*
>>>> --
>>>> Gromacs Users mailing list
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>>>
>>> --
>>> Shreyas Sanjay Kaptan
>>> --
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>>
>>
>> --
>> *Regards,*
>> *Rahul Suresh*
>> *Research Scholar*
>> *Bharathiar University*
>> *Coimbatore*
>>
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
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