I got this error when I imported openmm

anaconda3/lib/python3.10/site-packages/zmq/backend/cython/../../../../.././libstdc++.so.6: version `GLIBCXX_3.4.30' not found..

what is the problem?

Thank you, I got the answer for my question.
I think it is possible to meet some output.pdb, its frames have different atoms or elements............?
How can we define them like position !

Highlighting of the positions of atoms in each model is a goal of my project. Say I have 20 models(same atoms, but distributed differently). I think I have to cut my output.pdb into 20 modelxs.pdb then get every model then get its coordinate like: X = [float(coord[0]/nanometer) for coord in modelxpd...

This means that I have to cut the output files to many files every file contains positions for every model?
By the way I have used pandas, and it counts number 10 and more or -10 and less as positive whatever their signs.

Hi,
I got an output file from simulation of pdb file.
The output.pdb contains 20 models.
I want to be able to loop over positions and elements for every model. How can select certain model?

The pdb file has 2 types of residues "COR and EGH" in 1 chain "A" I define the residues like: <Residue> <Residue name="COR" > C................ </Residue> <Residue> <Residue name="EGH" > C................ </Residue> Then I am getting the error: anaconda3/envs/opki/lib/python3.10/site-packages/openmm...

What is the difference between the amber force field for linear and branched structures?

I successfully add the force block for a linear one, and it works. But I can not do a modified xml file to get the pdb file of the branched polymer get accepted by the program. I think I have to understand deeply how bonds types are written there. For that chain:(just an example ) (CHO2)(CH3)(CH3) E...

I am developing an amber force field for a branched polymer, but so far it did not work.
I am looking for any source helping me to understand <HarmonicBondForce>,
<HarmonicAngleForce> and <PeriodicTorsionForce>.

Best,
Elsaid

I was trying to reinstall open mm in my Linux pc, I got these errors after three hours: ~$ conda install -c conda-forge openmm=7.7.0 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: fai...