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

[Arron Lacey]

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?

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.
>