[gmx-users] RMSD analysis of protein-ligand complex

[Justin Lemkul]

On 10/5/19 11:11 AM, Quin K wrote:
> To see if complex is stable and to see how it fluctuate in the binding
> site.

Stability of the complex can mean multiple things. If you want to show 
that the protein structure is stable in the presence of the ligand, you 
would compute the RMSD of the protein (probably backbone) and compare 
the result against that of an apo simulation. If you want to show that 
the complex is stable in terms of the association of the protein and 
ligand, that's not something you do via RMSD; you compute distances, 
angles, etc. related to the interactions of the protein that hold the 
ligand in the active site.

You need to define what "it" is in the context of fluctuations. 
Fluctuation of the ligand in the binding can be computed by calculating 
RMSD of the ligand after a fit to the protein (to get relative motion). 
You can also do RMSF (e.g. of binding site residues, again to be 
compared against apo data for context/control).

-Justin

> On Sat, Oct 5, 2019 at 8:33 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/5/19 10:53 AM, Quin K wrote:
>>> Hi,
>>>
>>> *What should I pick for RMSD analysis of protein ligand complex? *
>>> *What other analysis can be done for protein ligand complex? *
>>> Following are the options I have for least square fit and for RMSD
>>> calculation.
>>> MPPA is the ligand I used.
>>> Group     0 (         System) has 50085 elements
>>> Group     1 (        Protein) has  4590 elements
>>> Group     2 (      Protein-H) has  2307 elements
>>> Group     3 (        C-alpha) has   282 elements
>>> Group     4 (       Backbone) has   846 elements
>>> Group     5 (      MainChain) has  1127 elements
>>> Group     6 (   MainChain+Cb) has  1396 elements
>>> Group     7 (    MainChain+H) has  1399 elements
>>> Group     8 (      SideChain) has  3191 elements
>>> Group     9 (    SideChain-H) has  1180 elements
>>> Group    10 (    Prot-Masses) has  4590 elements
>>> Group    11 (    non-Protein) has 45495 elements
>>> Group    12 (          Other) has    31 elements
>>> Group    13 (            MPPA) has    31 elements
>>> Group    14 (             NA) has     2 elements
>>> Group    15 (          Water) has 45462 elements
>>> Group    16 (            SOL) has 45462 elements
>>> Group    17 (      non-Water) has  4623 elements
>>> Group    18 (            Ion) has     2 elements
>>> Group    19 (            MPPA) has    31 elements
>>> Group    20 (             NA) has     2 elements
>>> Group    21 ( Water_and_ions) has 45464 elements
>>> Group    22 (    Protein_MPPA) has  4621 elements
>>>
>>> Thanks & regards!
>> What is your objective in calculating RMSD?
>>
>> -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

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