PyLipID
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wlsong
A python toolkit for analysing membrane protein-lipid interactions.
TypeError: object of type 'NoneType' has no len(). how can I resolve this issue for getting lipid interactions? Thanks, Arvin
Hello, Due to a change/removal of some of Numpy's aliases in the latest version(1.24), some calculations fail to run. For example, `li.collect_residue_contacts()` fails with the following error: "AttributeError: module ‘numpy’...
I'm simulating a CG version (Martini3) of a Glycine-Receptor in a POPC membrane with some THC molecules that I've parameterized myself. When I try to run the demo script that...
Hi there, I saw someone using PyLipID at the Biophysical Society Conference 2023 and wanted to give it a try but unfortunately I'm getting the following error at the first...
Hi everyone, I used the [demo script ](https://pylipid.readthedocs.io/en/master/demo.html) to analyze lipid interactions for varying concentrations of PODG (diaglycerol). For performance, I have deleted all water molecules in the xtc file...
Dear PyLipID developers, I am recently having issues when running PyLipID on my local workstation. My workstation has 12 CPUs, but with "num_cpus=None", PyLipID uses only 4 CPUs, and with...
I am working on the system with a heteromeric protein (two type a subunits, two type b subunits and one type c subunit). Is it somehow possible to get the...
It does not read my gro file and my trajectory despite the fact that I deleted water to make it faster. It freezes at collect from trajectories
When loading a large trajectory I receive the error ``` --------------------------------------------------------------------------- MemoryError Traceback (most recent call last) /tmp/ipykernel_1511828/2176272352.py in ----> 1 li.collect_residue_contacts() ~/Library/miniconda3/envs/BALMP/lib/python3.9/site-packages/pylipid/api/api.py in collect_residue_contacts(self) 331 for traj_idx in trange(len(self._trajfile_list),...
