www.neuron.yale.edu

I was trying to compile a neuron model for calcium diffusion with a calcium pump and a calcium channel present. I used the following files

cachan.mod
cadifusl.mod
capmp.mod

(the last two are from the "How to Expand Neuron's Library of Mechanisms" article from chapter 9 of the Neuron book)

and inserted them directly into a CA1 pyramidal neuron. However, I get an error somewhat like "cai is being written to the same spot by cadifusl.mod and capmp.mod" Does the calcium pump mechanism include calcium diffusion already?

Also, are there ways to cause channels on the plasma membrane to open due to ligands instead of voltage/current changes? If so, where can I find information on this?

(also, just of our curiosity, has anyone created a publicly available calcium channel that is not dependent on voltage?)

Thanks for your help.

srahim2 wrote:I get an error somewhat like "cai is being written to the same spot by cadifusl.mod and capmp.mod"

In any given section, only one mechanism can WRITE a particular ionic concentration.
Doesn't make sense to allow two different mechanism to do that, now, does it?

Does the calcium pump mechanism include calcium diffusion already?

Three points here:
1. It is natural to assume that file names define file contents unambiguously. But unless
you say where you found these files, only you can be sure about their contents.
2. From the previous answer, you now know that the problem lies in the fact that two
mechanisms that WRITE cai have been inserted into the same section.
3. WRITE conflicts have nothing to do with whether neither, one, or both of the
mechanisms contain a representation of diffusion. But you should be able to discover
which of these three alternatives is true by reading the NMODL source code yourself.
Do you see a KINETIC scheme, or one or more differential equations, that represents
exchange of solute between compartments?

Also, are there ways to cause channels on the plasma membrane to open due to ligands instead of voltage/current changes? If so, where can I find information on this?
(also, just of our curiosity, has anyone created a publicly available calcium channel that is not dependent on voltage?)

Try the likely places--mod files that accompany NEURON, and ModelDB.
See https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=11
At the very least you'll find some Ca-gated K conductances.

State transitions in the ChannelBuilder can be ligand-dependent. In the
ChannelBuildGateGUI, click on the Properties radio button. Select a transition, then
click on EquationType / alpha,beta / Ligand
and you can select from existing intra- and extracellular concentrations, or set up a
"new ligand".