Reaction with multiple substrates and products

[Gia Shelp]

Hello,

I am new to Copasi, but I have been following the manual and instructions, and I seem to be running into a minor issue.

I have multiple reactions that have 2-3 substrates and products, with all being recognized as species. These species are used in multiple other reactions and are the first few reactions in the pathways I am creating.

For example of the pathway:

[1] X -> A

[2] A + B + C -> D + E + F

[3] C + G -> H + I

When running the task, Time Course, these reactions will not trigger, leading to an accumulation of A.

I would love to get some idea as to why this is occurring, or if I am writing it incorrectly.

Thanks regardless,

Gia

[Hoops, Stefan (sh9cq)]

Hello Gia,

1) Check that all initial concentrations are not zero
2) Check that the kinetics you choose for your reactions are non-zero

I hope that helps!
Stefan

--
Stefan Hoops, Ph.D.
Research Associate Professor
Biocomplexity Institute & Initiative
University of Virginia
995 Research Park Boulevard
Charlottesville, VA 22911

Phone: +1 540 570 1301
Email: sho...@virginia.edu

[Gia Shelp]

Hi Stefan,

Thank you for your quick reply. I double checked, and yes, all my concentrations and kinetics seem to be non-zero. The issue is still occurring. All reactions with one substrate and product are running correctly (increasing/decreasing), however, reactions with more substrates and products are not activating, and the species concentrations are not changing. I will continue to play around with the model.

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Gia Shelp