On 7/24/13 6:44 AM, David van der Spoel wrote:
On 2013-07-24 01:57, Jonathan Saboury wrote:
I just finished this tutorial and found it very informative:
http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
However, This was based on a complex from a pdb.
I was wondering if it was possible to just simulate the protein without
complex and put the ligand as a solute and actually have it complex with
the protein. Obviously, if it could do this it would take a much longer
time than just simulating a complex, but if given enough time, could it
complex?
Yes, there are some examples. A paper was published by Shaw and co-worker in J.
Amer. Chem. Soc. a year or two ago.
I have no formal experience with simulations and currently have no one
around me with enough knowledge on these topic to mentor me, so any help is
very much appreciated!
For the rest of us mere mortals who don't have access to specialized hardware
that allows for 10- or 20-microsecond simulations, the brute force approach is
rather futile. Techniques like steered MD and Hamiltonian replica exchange MD
are probably more feasible. Unbiased simulations of sufficient length, using
"standard" supercomputing hardware, would probably take years.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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