On 8/22/13 3:25 PM, MUSYOKA THOMMAS wrote:
Dear users,
I am dealing with molecular docking of ligands to cysteine proteases and i
got several questions to pose.
1) For example looking at the structure of Falcipain-2 (PDBID=2OUL), i can
see it got several water molecules. when and how do i determine whether i
should stripe off the molecules. According to
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html,
i should check if the the catalytic site has water molecules. How do i
determine this?
You need to do background reading about the enzyme, its mechanism, and the
specific structure that you are using.
I removed the waters from lysozyme for that tutorial to avoid confusion that
would undoubtedly arise from multiple SOL entries after genbox and then the
choice of group for embedding ions. In general, one should not necessarily
dismiss crystal waters. There's probably never any harm in keeping them.
2) I got a cysteine PDB structure and a docked ligand PDB. How do i combine
the two to make one PDB file that i can use as my starting structure for MD
simulations?
If you've done docking, you already have it. The coordinate file is not the
challenge, the topology is. Deriving parameters for an arbitrary small molecule
for an existing parent force field is an advanced topic, one that can require
weeks or months of work. You will have to invest considerable time reading
about the underlying theory of your chosen force field and how one goes about
deriving new parameters.
As for dealing with the complex itself, there's a tutorial for that:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
-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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