Szegedi Tudományegyetem - Ahol tudás és szándék találkozik

Offer No: SZTE/2014/PB03611

Deadline for submission of offers: July 4th, 2014 15:00

Estimated Date of delivery: 1 week ARO

Short specification of product:

Items as shown below:

A. Molpro academic update program 1 licence

Molpro academic research group licence, parallel execution.

 

The program is licenced for use by a single research group and may be installed on any number of computers. A research group consists of a single designated research group leader and colleagues working under his / her direct supervision. The software can be executed in parallel on a multiprocessor machine. Source code is provided to allow installation on any supported architecture. The use of the software is restricted to non-commercial research.

 

B. AMBER 14 Software 1 licence

The release consists of about 50 programs that work reasonably well together. The major programs are as follows:

sander: Simulated annealing with NMR-derived energy restraints. This allows for NMR refinement based on NOE-derived distance restraints, torsion angle restraints, and penalty functions based on chemical shifts and NOESY volumes. Sander is also the "main" program used for molecular dynamics simulations, and is also used for replica-exchange, thermodynamic integration, and potential of mean force (PMF) calculations. Sander also includes QM/MM capability.   pmemd: This is an extensively-modified version (originally by Bob Duke) of the sander program, optimized for periodic, PME simulations, and for GB simulations. It is faster than sander and scales better on parallel machines. and it includes NVIDIA GPU acceleration. In the code model we are now following, sander is the vehicle to explore new features, and pmemd is a "production" code that implements sander's most-used features in a well-tested fashion that performs well in high-performance environments.   NAB: Originally named as "nucleic acid builder", NAB is a specialized language for writing programs that manipulate molecules and carry out molecular mechanics or distance-geometry based modelling. NAB provides and interface to Poisson-Boltzmann and RISM integral-equation solvent models. The "amberlite" package uses NAB to study protein-ligand interaction energetics.

LEaP: LEaP is an X-windows-based program that provides for basic model building and Amber coordinate and parameter/topology input file creation. It includes a molecular editor which allows for building residues and manipulating molecules.   antechamber: This program suite automates the process of developing force field descriptors for most organic molecules. It starts with structures (usually in PDB format), and generates files that can be read into LEaP for use in molecular modelling. The force field description that is generated is designed to be compatible with the usual Amber force fields for proteins and nucleic acids. The MCPB code can assist in generating force fields for metal centres.   ptraj and cpptraj: These are used to analyse MD trajectories, computing a variety of things, like RMS deviation from a reference structure, hydrogen bonding analysis, time-correlation functions, diffusional behaviour, and so on.   mm_pbsa and mmpbsa.py: These are scripts that automate post-processing of MD trajectories, to analyse energetics using continuum solvent ideas. It can be used to break energies into "pieces" arising from different residues, and to estimate free energy differences between conformational basins.

Evaluation principle: the lowest price


Offers are to be submitted by uploading your offer in PDF file (please click on „Upload Proposal”” in the top right corner).
More information:

• The purchase will be financed by TÁMOP-4.2.2.C-11/1/KONV-2012-0010 project.

• The offer price should include all the expenses (e.g. shipping to Szeged, Hungary; handling etc.) of the purchase.
  

• The quotation should also include the terms of delivery.

• Partial offer can also be accepted (A or B).
  

For further information please turn to the following official contact person:

Lajkóné Takács Ibolya foreign sales representative

E-mail: lajkone.takacs.ibolya@gmf.u-szeged.hu

Contact person for technical support: Bela Viskolcz dr., Faculty of Education, Department of Chemistry and Chemical Informatics, tel: +36 (62) 544-720, +36 (62) 544-000/4720, +36 (62) 546-224, +36 (62) 544-000/6224

email: viskolcz@jgypk.u-szeged.hu

The official language of the procedure is Hungarian, but offers can also be submitted in English language. The Inviting Authority expects offers from suppliers that can guarantee a prompt delivery and have a stable financial background. The Inviting Authority reserves the right to request further information from candidates within 5 working days in writing . Request for further information will be sent to each candidate with a valid offer. Following the submission deadline, the Inviting Authority evaluates the offers and candidates are informed on the result with the least possible delay.

The Inviting Authority reserves the right to cancel the above offer procedure fully or partially, without any justification. The Inviting Authority is not liable for consequences resulted by the withdrawal.

This call for proposal is not to be considered as a contractual commitment undertaken by the Inviting Authority. The call and the full procedure are subject to the Inviting Authority’s internal regulations.

Winner supplier: University College Cardiff Consultants Ltd
Winner price: 980 550 HUF + VAT

Winner supplier: University of California, San Francisco
Winner price: 114 330 HUF + VAT