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

[Justin Lemkul]

On 10/5/19 11:24 AM, Quin K wrote:
> Thank you!
> How important is the least square fit in these RMSD calculations?

Very; it determines how to interpret the result.

> Or should I just pick system for least square fit all time?

You should never pick "System" for a fit.

-Justin

> On Sat, Oct 5, 2019 at 8:45 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
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>> * Please search the archive at
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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

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