On 10/5/19 1:58 PM, Quin K wrote:
Thank you.
I examined the trajectory using VMD and noted that ligand had come out of
the binding site and is running around.
How is this possible? I have used the guidelines in mdtutorials.com to set
up the system.
However it's worth noting that there was a power failure around the same
time (23ns) and I had to restart MD with append command.
Could this have had an affect on MD? Do I have to recreate trajectory file
after restarting MD, instead of using the default trajectory?
I imagine it's possible that the power failure caused a corruption in
some file, and it's too much of a coincidence that just when the power
failed, your simulation changed radically. I would re-run it.
Also note that a ligand can dissociate from the binding site if the
topology is not well parametrized, leading to insufficiently strong
interactions. You shouldn't likely encounter such a problem if you get a
reasonable CGenFF topology, but it's worth noting as a general problem
with any ligand parametrization.
-Justin
Regards
On Sat, Oct 5, 2019 at 9:53 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 10/5/19 11:59 AM, Quin K wrote:
Thank you.
I got following when I analysed Ligand RMSD protein backbone as east
square
fit.
Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7>
Can you please comment why there's high fluctuation after like 23 ns?
What could this mean?
Watch the trajectory and see what is going on. Make sure you've properly
re-imaged to account for PBC effects.
-Justin
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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