[gmx-users] RMSD analysis of protein-ligand complex
Justin Lemkul
jalemkul at vt.edu
Sat Oct 5 17:38:16 CEST 2019
On 10/5/19 11:36 AM, Quin K wrote:
> OK thanks.
> What should I pick for least square fit in following instances for example.
> *RMSD of*
> 1. protein backbone+ligand
> 2. protein backbone
> 3. lingad only
I've already answered that. And again, it always depends on the question
you are asking. You want the change in a structure relative to
something. What is that something and how can you justify (to yourself
and your reviewers!) that choice?
-Justin
> On Sat, Oct 5, 2019 at 8:56 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> 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
>>>>
>>>> ==================================================
>>>>
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>>>> 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * 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
==================================================
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