Joshua Soon

Change title font size and add label for X-axis in barplot of enrichResult?

2

Hi YuLab, I am trying to change the font size for the title of the barplot generated by this function but there doesn't seem to be an argument for this,...

PDBIO.save() include SEQRES information?

4

### Setup I have a question regarding Biopython version, Python version, and operating: ```python Python 3.9.12 (main, Jun 1 2022, 11:38:51) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help",...

Water molecules go out of bounding box while running MD

1

Hi openmm developers, I was trying to run a simple MD simulation to fold a small peptide of 10 amino acids in length, and loading the PDB file directly with...

Select residue atom positions for residues with alternate locations (altloc)

2

Hi developers of PDBfixer, I was wondering, how do I select which one of the alternate locations (altloc) of a residue to retain in the fixed PDB? For example in...

XYZ to SDF no formal charges

4

## Environment Information Open Babel version: ``` # Name Version Build Channel openbabel 3.1.1 py310h956b46e_7 conda-forge ``` Operating system and version: ``` Distributor ID: ManjaroLinux Description: Manjaro Linux Release: 23.0.0...

PBC conditions increase memory consumption by more than 20 times

1

Hi developers of `torchANI`, I was trying to run some MD simulations of a really small protein, a 10 peptide Chignolin protein with a 4Å buffer water-box which is about...

How is allegro trained with forces? And are there available weights for running full scale MD simulations?

1

Hi developers of Allegro, I have two questions namely on the methodology behind allegro and it's applications: 1. In the Nature communications publication, the model's architecture is depicted [as such](https://www.nature.com/articles/s41467-023-36329-y/figures/1)...

Support for simulations with multiple small molecule ligands

4

## Overview I am trying to run a simple NPT simulation with multiple ligands from a single SDF file parameterised with GAFF but I am running into `ValueError`s for multiple...

Question on which specific database contains energy and forces

2

``` In this work, we aim to aid the training of Hamiltonian-predicting models and NNPs for druglike molecules by significantly extending and improving the nablaDFT dataset [11]. We double the...

Converting Psi4 (or other QC tools) electron densities to spherical harmonics

1

I was wondering is there a way whereby the electron densities from Psi4's wave function objects can be fitted to spherical harmonic basis functions and if this could be generalised...