[gmx-users] centroid distance for tyrosine

[Justin Lemkul]

On 2/16/19 2:01 PM, Archana Sonawani-Jagtap wrote:
> Hi Justin,
>
> I think something is wrong in the command because when I visualize the
> distance between OH atoms of tyrosine's in VMD it shows ranging from 3 to
> 10 ang. Also, when I take single frame in pdb format and check centroid
> distance using PIC webserver, it gives within same range. However, using
> above command it gives distance within 1.37-1.38 ang.
>
> I used following command:
>
> gmx distance -f apo-cxcr4-final1.xtc -s mdmodified_cxcr4.tpr -n
> nter_index.ndx -oav distave_tyr12-21.xvg -select 12Y_cog  21Y_cog -oall
> dist_tyr12-21.xvg
>
> What could be wrong?

You didn't use the syntax I gave you (and I'm not sure how what you 
provided is even a valid command).

gmx distance is giving you what you asked for, all distances (-oall) in 
the groups provided, so you're seeing values that are consistent with 
C-C bond lengths.

-Justin

>
>
>
>
> On Sat, Feb 16, 2019 at 4:31 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 2/15/19 2:37 PM, Archana Sonawani-Jagtap wrote:
>>> Hi,
>>>
>>> I want to calculate centroid distance between 2 tyrosine rings throughout
>>> the simulation. Which option of gmx distance can help to plot the
>> centroid
>>> distance?
>> Create two index groups with the ring atoms, then use gmx distance:
>>
>> gmx distance -s -f -select 'cog of group "ring1" plus cog of group "ring2"'
>>
>> -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

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