Software

 
 Alchemify: An X-PLOR PSF post-processor for alchemical free-energy calculations in NAMD. Alchemify is a small program that handles nonbonded exclusion lists and remove unwanted bonded terms, which appear in the definition of hybrid dual topologies.
 
Novel free-energy developments in NAMD are reported on the web site of the Theoretical and Computational Biophysics Group at the University of Illinois, Urbana-Champaign. Specific information about the adaptive biasing force method can be found on the ABF website.
     
 

- Molefacture: The Molefacture plugin provides VMD users with an interface to edit molecules. This includes the ability to add, delete, or manipulate their structure at an atomic level, and to build new components from a library of common fragments. It also offers a front-end for the setup of alchemical free-energy perturbation calculations.

- ParseFEP: ParseFEP consists of a set of tools for the analysis of free-energy perturbation calculations carried out within NAMD.

- Mutator: Mutator is a tool for mutating a target residue selected by its segment name and id, and the three character residue code for the mutant amino acid. It can also build, for the specific purpose of alchemical free-energy calculations, a hybrid structure where both the initial and mutated side chains are present. It features a library of all possible amino-acid hybrid dual topologies. 
     
 
 Optimally Partitioned Electric Properties: A tool for the derivation of models of distributed multipoles and polarizabilities. Using local frames of reference, OPEP determines distributed multipoles up to hexadecapoles from the molecular electrostatic potential, and distributed, isotropic or anisotropic polarizabilities up to quadrupolar from the induction energy mapped spatially around the molecule of interest.

 

Recent publications

Bignon, E.; Gattuso, H.; Morell, C.; Dehez, F.; Georgakilas, A. G.; Monari, A. & Dumont, E.
Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion.
Nucleic Acids Res.

2016,  (44), 8588-8599.
dx.doi.org

Wang, S.; Zhao, T.; Shao, X.; Chipot, C.; Cai, W.
Complex movements in rotaxanes: Shuttling coupled with conformational transition of cyclodextrins
J. Phys. Chem. C

2016,  (120), 19479-19486.
dx.doi.org

Gattuso, H.; Durand, E.; Bignon, E.; Morell, C.; Georgakilas, A. G.; Dumont, E.; Chipot, C.; Dehez, F.; Monari, A.
Repair rate of clustered abasic DNA lesions by human endonuclease: Molecular bases of sequence specificity
J. Phys. Chem. Lett

2016,  (19), 3760-3765.
dx.doi.org

News

- Renewal of the Laboratoire International Associé CNRS-University of Illinois at Urbana-Champaign on November 2016
- An update of ParseFEP is available in the latest version of VMD.
- 新的分子动力学讲义 (Dissemination).
 

Contact

Laboratoire International Associé
CNRS-UIUC
Unité mixte de recherche n°7565
Université de Lorraine, B.P. 70239
54506 Vandoeuvre-lès-Nancy Cedex, France
 
Phone: +33.(0)3.83.68.40.97
Fax: +33.(0)3.83.68.43.87
 
How to reach us