[gmx-users] does gromac "mdrun" produce predicted 3d structure?

[Justin Lemkul]

On 1/22/16 9:35 AM, Arron Lacey wrote:
> Thanks Justin - you mention
>
> "You need actual (extensive) MD simulations to determine that"
>
> I suppose what I am after is - what software is capable of providing such MD
> simulations?
>

You've already come to the right place...

-Justin

> Thanks!
>
>
>
> On 22/01/16 13:13, Justin Lemkul wrote:
>>
>>
>> On 1/22/16 8:05 AM, Arron Lacey wrote:
>>> Hi everyone - I have used I-TASSER to generate pdb files for missense SNPs. I
>>> understand there are some reservations about the accuracy of SNP structural
>>> changes by using homology based methods alone. Can GROMACS off anything better?
>>> I have used
>>>
>>> gmx mdrun <options>
>>>
>>> to calculate the energy minimization of the pdb files that I-TASSER outputs, but
>>> I want to know if mdrun can produce the predicted co-ordinates of the structure
>>> due to the SNP (if there is any change that is)?
>>>
>>
>> There is no really simple answer to this, but here are a few things to
>> consider.  GROMACS does not predict structures.  It calculates the physical
>> forces on the given configuration according to whatever instructions you
>> provide.  Energy minimization is certainly insufficient to establish whether
>> or not your mutation is structurally reasonable.  You need actual (extensive)
>> MD simulations to determine that.  More importantly, the quality of the
>> simulation is only as good as the force field you apply for the simulation.
>> All force fields involve assumptions and have some inaccuracy.  So your
>> ability to "predict" using GROMACS (I suggest you don't use that term in this
>> context) is only as good as (1) the rigor of the method you apply via the MD
>> and (2) the quality of the force field in discriminating subtle behaviors.
>>
>> -Justin
>>
>>> Also - does there a better way to embed a SNP in a wild-type pdb file for input
>>> to pdb2gmx?
>>>
>>> Thanks very much.
>>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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