Nazanin Donyapour

fix add missing unknown (UNK) residues error

3

Hello, I am trying to run pdbfixer with these arguments `pdbfixer --pdbid=6fs0 --add-atoms=all --replace-nonstandard --add-residues --replace-nonstandard` but I ran into the error below. It seems that pdbfixer tries to add...

pdb2pqr modifies the chain names

4

Hello, I'm utilizing `pdb2pqr` to add hydrogens to my structure with the following arguments. ``` pdb2pqr --ff='AMBER' --ffout='AMBER' --with-ph=7.0 --drop-water --pdb-output complex_h.pdb receptor_pdb4amber.pdb complex_h.pqr ``` However, I observed that in...

Hello, I'm trying to reproduce the pKa predictions for several structures in the [OnionNet_Core_2016](https://github.com/zhenglz/onionnet/blob/master/datasets/output_v2016_predicted.csv) test set, but the values I'm getting differ from those in the paper. Attached is a...

HDF5 file reading error

5

Hello, I recently installed `wepy` from pip. I had some issues when I tried to run my simulations so I updated `h5py` and `networkx`. I ran into "Type names and...