Chih-Ying Lin wrote:
HI
I am simulating the protein + ligand + water molecules system.
In the experimental work, the concentration of ligand is pretty low, say
under 20 mM (avearge 18 ligands attached on one protein)
It will be a huge system to create a system with 20 mM and it will take
lot of simulation time.
Instead, I create a 6nm x 6nm x 6nm simulation box and put one protein
molecule with 10 ligands.
After 100 nano seconds, 10 ligands are attached on the protein.
Then, for this one protein with 10 ligands attached + water molecules
I will do the following steps =>
1. remove the water molecules
2. center the protein with 10 ligands attached in the 6nm x 6nm x 6nm
simulation box
3. put another 10 ligands around the protein with 10 ligand attached
4. solvate the system
5. add ions
Are the above steps make sense to create a low concentration simulation?
Seems vaguely plausible. The problem with reproducing a bulk
concentration of a minor species is that it was normally measured when
the ratio of solvent volume to (e.g.) protein volume was extremely
large, and a simulation can't afford that. For trying to reproduce
experimental conditions with small volumes, you need to know about the
protein/bulk-solvent "interfacial" concentration, which is hard to study
experimentally. Traditionally, you guess something plausible and hope
for the best... preferably a range of plausible choices and see what you
find.
Mark
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