Time course error

[George]

Hello,

i have this error when i run time course:

>EXCEPTION 2022-02-24T17:10:44<

CTrajectoryMethod (6): Deterministic integration failed. LSODA reported:

DLSODA- At current T (=R1), MXSTEP (=I1) steps

taken on this call before reaching TOUT

In above message, I1 = '100000'

In above message, R1 = '1.31778e-95'

Please see result for indications of numerical instability.

How can i solve this?

This is my copasi model

Thanks.

[sven....@gmail.com]

Dear George, 

after only briefly looking at the model my impression is that the name  "2.8.1.8" for a substrate in the rate laws is a problem. I think it is possible in COPASI to use this name for a species (although I would probably avoid it), but it seems that COPASI does not like it as a name in the mathematical expression of a rate law.  

Did you enter the model yourself in COPASI, or was it imported from some other software?

Sven

[George]

i made this model in python, i generated the sbml and i imported it.

where can i put the enzyme 2.8.1.8 in sbml? I put it into the list of reactants of a reaction, this maybe the problem...

[Hoops, Stefan (sh9cq)]

Hello George,

You can have a species with the name 2.8.1.8. As function parameter
parameter however this is currently not possible. I modified the
functions to use enzyme as the name of the parameter. Please see the
attached file.

The problem with the failed integration is division by 0 in your
functions: (1 - 1/1) * ... = 0

I would appreciate if you could send me the original SBML file as the
import created invalid functions so that I can fix this problem.

Thanks,
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

[George]

i would like set the value of substrate to 1 in my model and define my kinetic law as: enzyme*kcat_parameter*(substrate/k_parameter)^stoichiometry of substrate/(1-(substrate/k_parameter)^stoichiometry of substrate)

[Hoops, Stefan (sh9cq)]

Hello George,

Thank you for the SBML file! I noticed that it is invalid SBML the id
of a species must not include '.' COPASI still loads it since we use
names which do not have the same restrictions. You can fix this by
using both name and id in SBML. Note the id must be of the form:

letter ::= ’a’..’z’,’A’..’Z’
digit ::= ’0’..’9’
idChar ::= letter | digit | ’_’
name ::= ( letter | ’_’ ) idChar*

The following would be valid:
<species id='_2_8_1_8' name='2.8.1.8' compartment='C' ...

There are several problems with your rate law:
1) division by zero if substrate == k_parameter
2) negative if substrate > k_parameter

Where did you find it? Normally you would see the form
1 + (substrate/k_parameter)^stoichiometry
^
which would avoid both problems.

Thanks,
Stefan

[George]

Ok thank you! I solved, now how can i set the value of a substrate on sbml?

[George]

Now when i run time course, the generated plots are so flat,  are monotonous.

Values don't vary with the time after start.