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
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.
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