UNRESPACK v. 3.2 - a package to run united-residue protein simulations with the UNRES force field. It is a successor of earlier more specific version of UNRES to predict protein structure by global optimization (v. 1.0) and of the molecular dynamics version (version 2.0).
The package has the following directory structure:
Before downloading this package you must agree on the License Terms as stated below.
LICENSE TERMS
This software is provided free of charge to academic users, subject to the condition that no part of it be sold or used otherwise for commercial purposes, including, but not limited to its incorporation into commercial software packages, without written consent from the authors. For permission contact the authorities of Cornell Univesity and University of Gdansk.
This software package is provided on an "as is" basis. We in no way warrant either this software or results it may produce.
Reports or publications using this software package must contain an acknowledgment to the authors and the NIH Resource in the form commonly used in academic research.
To access UNRES, or "UNRES scale-consistent", "UNRES phosphorylated", "UNRES dock" and "SUGRES" versions of UNRES: you must accept the terms above.
The archive contains the following:
-- the source code with the addition of the SUGRES-1P module (sub-directory "source")
-- parameter files (sub-directory "PARAM")
-- a working example for the coarse-grained molecular dynamics of Heparin dp24 (files hp_dp24.pdb, hp_dp24.inp in the sub-directory "example") together with the corresponding outputs (sub-directory "example/OUTPUTS")
The SUGRES-1P force field is based on the theoretical model described in Lubecka, E.A., & Liwo, A. J. Chem. Phys.,147(11) 115101 (2017) and in Samsonov, S.A. et al., Biopol., (2019).
UNRES-XLINKS. Version of UNRES with molecular dynamics algorithm changed to handle large systems and with the latest
addition for data-assisted simulations. For full description see: description page.
This is a new version with a five-band inertia matrix, which saves considerable memory and enables the user to run >50,000 residue systems, which also includes a new algoritm od handling NMR data at the coarse-grained level. The dimension is presently 10,000 residues; to change this, change the statement
parameter (maxres=xxxxx) in the DIMENSIONS file in all source directories.
Parameters of the force field and parameters for NMR-data-assisted calculation with the new ESCASA algorithm (E. Lubecka, A. Liwo, J. Comput. Chem., accepted).
UNRES-Dock. UNRES package with an extension for docking of two proteins or protein/peptide with random starting orientations.
An example docking is in unres/examples/UNRES-Dock directory. See: description and install manual.
Input files and initial and experimental reference structures used in testing of UNRES-Dock package.
New version of UNRES, local and correlation terms re-derived based on the new scale-consistent theory
(Sieradzan et al., J. Chem. Phys., 146, 124106, 2017)
and calibrated with 9 proteins (Liwo et al., J. Chem. Phys. 150, 155104 (2019); https://doi.org/10.1063/1.5093015)
2012-04-04: unres_MD source code tidied and uniform Makefiles for the 1GAB/4P and 1E0L_1L2Y force field created for gfortran (single-processor version) and ifort (single-processor and MPICH version) compilers.
2012-04-03: hotfixes and examples added
2014-12-11: Version 3.2.1 released. Sidecain-backbone torsionals introduced for the GAB and E0L2Y force fields. A number of bugs fixed, manuals revised. Minimization alone added (directory src_MIN and MINIM in the bin subdirectory)
2017-09-25: merge with prerelease 3.2.1
End of Changelog.
To uncompress a tar-gz file of a package say:
gzip -cd package.tar.gz | tar xf -
Each directory contains a README file to explain its contents.
NARES
This is a preliminary distribution of the NARES software for coarse-grained simulations of nucleic acids with the NARES-2P force field. The functions of the package are as follows:
Single energy evaluation
Energy minimization
Molecular dynamics and its REMD and MREMD extensions
Calculation of thermodynamics properties and conformational ensembles
Cluster analysis of conformational ensembles
Please refer to the UNRES manual and to the examples collected in the TESTS director for more detail; except for different sequence encoding the input format is the same.
Source code:
nares: main components of the package (MD, (M)REMD, energy evaluation and minimization). wham: weighted-histogram analysis of (M)REMD results. cluster: cluster analysis of the ensembles generated by (M)REMD and analyzed by wham. xdrf2pdb: produce pdb-format trajectories from compressed trajectory files (cx).
References:
Y. He, M. Maciejczyk, S. Oldziej, H.A. Scheraga, A. Liwo,
Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix.
Phys. Rev. Lett., 110, 098101, 2013
A. Liwo, M. Baranowski, C. Czaplewski, E. Golas, Y. He, D. Jagiela, P. Krupa, M. Maciejczyk, M. Makowski, M.A Mozolewska, A. Niadzvedtski, S. Oldziej, H.A. Scheraga, A.K. Sieradzan, R. Ślusarz, T. Wirecki, Y. Yin, B. Zaborowski.
A unified coarse-grained model of biological macromolecules based on mean-field multipole.multipole interactions.
J. Molec. Model., 2014, 20, 1-15.
You can download this preliminary distribution of the NARES software here.
Software for back mapping of all-atom structure form NARES-2P representation (lNARall) can be found here (last modified: Thu Nov 10 09:36:40 2022).
CREDITS TO DEVELOPERS OF CODES IMPORTED INTO UNRES
All programs use the fitsq subroutine written by Dr. Kenneth D. Gibson, Cornell University, retired.
The MD program uses the surfatom subroutine written by Dr. J.W. Ponder, Washington University.
The SUMSL subroutine (Gay, Assoc. Comput. Math. Trans. Math. Software, 9, 503-524, 1983, is used for minimization.
The CLUSTER program uses the hc subroutine developed by Dr. G. Murtagh, ESA/ESO/STECF, Garching.
UNRES, WHAM, CLUSTER, and XDRFPDB use the Europort Data Library (xdrf) developed by Dr. F. van Hoesel, Groeningen University, to write and read compressed data files.
Previous versions ("version 2") of the packages are available here.
