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 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
