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