Julien Michel
Julien Michel
We do occasionally work with glycoproteins is there a way to add this support so we can load these systems into BSS? I think using tleap and pdb4amber in BSS...
Currently, at least for somd, it appears it isn't possible to setup input files for a free energy calculation in one BioSimSpace script, and load the input and run a...
On the latest devel version BioSimSpace-2019.1.0+297.gd5cc5b7 the attached BSS script fails on this pair of input files with this error message ``` ~/biosimspace.app/bin/python custom_prepareFEP.py --input1 input/THROM\:throm_lig6a/* --input2 input/THROM\:throm_lig6b/* --output 6a_6b...
Currently we only support relative free energy calculations but absolute solvation free energy calculations are routinely carried out in the field with well described protocols. @lohedges @ppxasjsm how much work...
As far as I am aware Sire doesn't currently have data structures to describe virtual sites. Virtual sites are becoming more and more popular and are found in a growing...
Dear pymbar developers, Is there a plan to support linux-aarch64 packages on conda-forge for pymbar (preferably
The move to 2023 seems to have broken SOMD. The example below attempts to carry out an RBFE calculation on a protein-ligand system. I am using [feature_pmefep_2023](https://github.com/michellab/Sire/tree/feature_pmefep_2023) ; Sire version:...
The exact Sire version used is no written in the SOMD outputs. This would be useful for debugging purposes.
The 'old' SireIO:Amber() object that implements readCrdTop() is still needed because the new parser doesn't create a SIreMol::AmberParameters object for each loaded molecule. This object is needed for initialising an...
Hi @JenkeScheen , A few comments/questions after going through your setup notebook: - The notebook assumes the user has access to parameterised ligands (in vacuum) that have coordinates matching those...