Sukrit Singh
Sukrit Singh
This is a feature request only but it'd be really cool if the YAML input to Perses could support Protein Mutation setups. Presently, setting up the mutation-oriented HTFs is done...
In setting up a metadynamics simulation with a system and state file, I was hoping to be able to setup a simulation using a dihedral and a pair of distances...
It's been brought to my attention that folks who are using `md.load_dtr()` to load DTR files are often times using CMS topology files that are auto-generated and not using a...
Noting down YANK issues as I've been encountering them recently with the OpenMMTools API shift: I'm encountering another example where setup runs fine but during the propagation/mixing steps the following...
Just wanted to report an issue + solution @ijpulidos helped me fix - noting it here for any future updates. **Problem:** Basically anytime I run something in YANK (after installing...
Basically my question is: Can perses handle mutation predictions in complexes that involve a cofactor/ligand bound in one chain? I have a system involving the study of Protein:Protein complex, using...
Hi! I've been setting up a few mutants to study the impact of a mutation in the context of a dimerization, and I have encountered a mutation case that appears...
This PR provides the following changes in reference to #259 : 1. Adds two new residue templates [SEP](http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=sep&operation=ccid) and [PTR](http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&target=ptr&operation=ccid) (pSer and pTyr respectively). Note that Hydrogens were removed from...
After discussing with @jchodera - and building on #218 - Is there any plans to add phosphorylated residues such as pSer and pTyr as templates? For setting up initial structures...
Here's an initial draft of 4 cookbooks for running enhanced sampling methods (AMD, GAMD, MetaD, and Umbrella Sampling) using OpenMM. Each of them are located in a subdirectory inside `cookbook/Enhanced...