Maciej Majewski

It matters most for Asn and Gln where O and N of the amid group have the same electron density and can sometimes be misinterpreted. also His but to a...

Does it take into account the ligand?

Hi! `data/train_fulldata/epoch=80.ckp` is a pretrained network that can be downloaded from: ```wget pub.htmd.org/torchMD_tutorial_data.tar.gz``` It is explained in the second cell of the tutorial https://github.com/torchmd/torchmd-cg/blob/master/tutorial/Chignolin_Coarse-Grained_Tutorial.ipynb The calculator can be used with...

Thanks for noticing the missing file. `*tar.gz` file have been updated. You can find the file by executing the first cells of tutorial: ``` wget pub.htmd.org/torchMD_tutorial_data.tar.gz tar -xvf torchMD_tutorial_data.tar.gz ```

1. We had some major updates to the code recently, so the old training code was moved to a separate repo: **torchmd-net-legacy**: https://github.com/torchmd/torchmd-net-legacy The net shared here was trained using...

I'm glad I could help. What is the error you get with training?

It looks like you need to export the path of "torchmd-net-legacy" to your pythonpath: ``` export PYTHONPATH="PATH/torchmd-net-legacy" ``` or edit it directly in your bashrc: https://bic-berkeley.github.io/psych-214-fall-2016/using_pythonpath.html If you don't do...

If you want to simulate multiple proteins in the same simulation box, torchMD can deal with that without an issue. The system is defined with a topology file and it...

Hi! There might be some issue with your moleculekit installation. Please check this issue: https://github.com/torchmd/torchmd-cg/issues/23