Project ID: plumID:23.031
Name: Identifying small molecules binding sites in RNA conformational ensembles with SHAMAN
Archive: https://github.com/maxbonomi/plumed-nest-data/raw/master/projects-2023/SHAMAN-benchmark/SHAMAN-benchmark.zip
Category: bio
Keywords: RNA, metadynamics, probes, mixed-solvent MD, small molecules, binding sites
PLUMED version: 2.10
Contributor: Max Bonomi
Submitted on: 06 Aug 2023
Publication: F. P. Panei, P. Gkeka, M. Bonomi, Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN (2023)

PLUMED input files

File Compatible with
1anr/00-APO/2-Production/plumed.dat tested on master
1anr/01-BENX/2-Production/plumed.dat tested on master
1anr/02-BETH/2-Production/plumed.dat tested on master
1anr/03-PRPX/2-Production/plumed.dat tested on master
1anr/04-DMEE/2-Production/plumed.dat tested on master
1anr/05-MEPY/2-Production/plumed.dat tested on master
1anr/06-BENF/2-Production/plumed.dat tested on master
1anr/07-MEOH/2-Production/plumed.dat tested on master
1anr/08-IMIA/2-Production/plumed.dat tested on master
1anr/09-PIRZ/2-Production/plumed.dat tested on master
1anr/10-FORM/2-Production/plumed.dat tested on master
1anr/11-MAMY/2-Production/plumed.dat tested on master
1anr/12-ACEY/2-Production/plumed.dat tested on master
1mfy/00-APO/2-Production/plumed.dat tested on master
1mfy/01-BENX/2-Production/plumed.dat tested on master
1mfy/02-BETH/2-Production/plumed.dat tested on master
1mfy/03-PRPX/2-Production/plumed.dat tested on master
1mfy/04-DMEE/2-Production/plumed.dat tested on master
1mfy/05-MEPY/2-Production/plumed.dat tested on master
1mfy/06-BENF/2-Production/plumed.dat tested on master

Last tested: 28 Feb 2024, 06:52:10

Project description and instructions
PLUMED input files to perform Shadow Mixed-Solvent MetaDynamics simulations. Simulations have been performed with the master branch of PLUMED available here and GROMACS 2021.5. All the GROMACS topology files are available here.

Submission history
[v1] 06 Aug 2023: original submission

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plumeDnest:23.031