[gmx-users] Energy Minimization
Mark.Abraham at anu.edu.au
Tue Jan 10 13:06:24 CET 2012
On 10/01/2012 10:46 PM, Steven Neumann wrote:
> Thank you. Imagine I would like to put ligands in further simulations.
> Should I then copy coordinates of my ligands in smaller box (not to
> overlap my tube) and then copy both coordinates of ions and ligands
> plus protein?
Any way you want to construct your non-overlapping non-solvent non-ion
molecules is fine. Previous EM of each is wise, but not necessarily
required - vacuo EM is probably fine. Then solvate, then use genion,
then EM the whole system. Copying ions from earlier calculations is a
good way to generate atomic clashes, which is a high price to pay for
randomly-placed ions that are different from those generated as above.
> On Tue, Jan 10, 2012 at 11:31 AM, Mark Abraham
> <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>> wrote:
> On 10/01/2012 10:13 PM, Steven Neumann wrote:
> Thank you. Should I also copy and paste coordinates of my ions
> or just my protein?
> The randomly-placed ions will be immaterial for EM.
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