New version of Modeller, 9.13

Radha Agarkar — Thu, 13 Feb 2014 09:07:57 -0600

The new version of Modeller, 9.13, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information.

If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9.13 - the same license key will work. (It won't do any harm to reregister if you want to, though!)

9.13 is primarily a bugfix release relative to the last public release(9.12). Major user-visible changes include:

# Modeller now includes a variety of SOAP (statistically optimized atomic potential) scores for assessing proteins, loops, and interfaces.

# The Lennard-Jones interaction energy is now artificially truncated at very short distance; this makes simulations with poor starting conditions much less likely to 'blow up'.

# model.get_insertions(), model.get_deletions() and model.loops() now have an include_termini option; if False, residue ranges that include chain termini are excluded from the output.

See the Modeller manual for a full change log: http://salilab.org/modeller/9.13/manual/node39.html

If you encounter bugs in Modeller 9.13, please see http://salilab.org/modeller/9.13/manual/node10.html for information on how to report them.

Reference:

http://salilab.org/modeller/

WSCC – 2013

Radha Agarkar — Sat, 09 Nov 2013 18:35:18 -0600

DST-SERB Winter School on Computational Chemistry (WSCC – 2013)

December 9-13, 2013

Organized By Department of Chemistry, Sardar Patel University, Vallabh Vidyanagar – 388120, Gujarat

Topics to be covered

The topics and lectures including practical sessions planned are summarized as follows:

Topics of Teaching and Research

1. Review of postulates of quantum mechanics; Some key concepts from linear algebra; The Schrodinger equation; Particle in one dimensional box; Hydrogenic orbitals; The helium atom; many electron; Problem solving. -

[Prof. R. B. Sunoj, IITB, Mumbai]

2. The Born–Oppenheimer Approximations; Qualitative MO Theory; Potential energy surfaces; Variational Theorem, Perturbation theory; Problem solving.

[Dr. Narahari Sastry, CSIR-IICT, Hyderabad]

3. Hartree Products; Slater determinants; Antisymmetry principle; The Hartree-Fock approximation; Restricted and Unrestricted Hartree–Fock; Koopmans’ theorem; Electron correlation; Electron density; Examples and problems.

[Prof. S. R. Gadre, IITK, Kanpur]

4. Hückel Theory, Bond order and charge density analysis; Extended Hückel Theory; Semi-Empirical Methods: e.g. CNDO; AM1; PM3; Parameterization; Advantages and Limitations of Semi-Empirical Methods. Applications.

[Prof. S. P. Gejji, Univ. Pune]

5. ab initio methods; Classification of Basis Sets; Conﬁguration Interaction; Møller–Plesset perturbation theory; Coupled Cluster theory; Solvation Models; Continuum Solvation Models.

[Dr. C. H. Suresh, CSIR- NIIST, Thiruvananthapurum]

6. Density Functional Theory: The Hohenberg-Kohn theorems; The Kohn-Sham equations; Local density and generalized gradient approximations; The LCAO Ansatz in the KS equations; Applications of DFT.

[Prof. M. S. Gopinathan, IISER, Thiruvananthapurum]

7. Hybrid or hyper-GGA methods; beyond static DFT; Beyond LDA and GGA; Self-interaction correction; Dispersion corrected functional; Time-dependent DFT (TD-DFT): Runge-Gross theorem; Conceptual DFT: Fukui function; Global hardness and softness; Local hardness and softness; Electronegativity and the Electronic Chemical Potential.

[Dr. D. K. Maity, BARC, Mumbai]

8. Molecular Mechanics

Introduction; Empirical Force Fields; Force Field Parameterization; Differences in Force Fields; Energy Minimization; Limitations of Molecular Mechanics Models.

[Dr. Sudhir Kulkarni, Vlife Technologies, Pune ]

9. Statistics and QSAR

Introduction; Elementary Statistical Measures; Correlation between Two Sets of Data; Correlation between Many Sets of Data; Quantitative Structure–Activity Relationships (QSAR); Structure property correlation; Molecular descriptors; Application in biological systems; 3D-QSAR

[Dr. Sudhir Kulkarni, Vlife Technologies, Pune ]

10. Qualitative Valence Bond Theory:

Roots of VB theory; The two-electron bond; Polyatomic molecules; hybridization; Writing and representing VB wave functions; Bridges between Molecular Orbital (MO) and VB theories; Applications.

[Prof. S. Ramashesha, IISc, Bangalore]

11. Molecular dynamics

Equations of Motion; Dynamics Trajectories: Integrating Newton's Laws; Ensembles; Periodic boundary conditions; Monte Carlo Methods; Classical and ab initio molecular dynamics; Applications.

[Dr. Nisanth Nair, IITK, Kanpur]

More Info : https://sites.google.com/site/dstserbwscc2013

BOL: Molecular Modelling and Drug Design's News

New version of Modeller, 9.13

WSCC – 2013