You are here

UNRES with new cross-links, NMR and SAXS

This distribution contains the version of UNRES, in which the molecular dynamics algorithm has been changed to handle large systems and with the latest addition for data-assisted simulations:

(1) Latest cross-link potentials dependent on the distance beween the side-chain ends involved and side-chain orientation (Kogut et al., J. Comput. Chem., in review). See the file xlinks.F in the source directories, the respective section of subroutine edis in energy_p_new_barrier.F (UNRES source directory), and the file xlinks_parameters.dat in the PARAM directory. For an example of cross-link assisted MD simulations see the examples directory, README file.

(2) The ESCASA algorithm for handling NMR restraints (Lubecka & Liwo, J. Comput. Chem., 42, 1579, 2021). See the file nmr_hpos.F in the source directories, the respective section of subroutine edis and the file nmr.parm in the PARAM directory.

(3) Improved function to calculate SAXS distance-distribution curves from coarse-grained geometry in SAXS-assisted simulations. See subroutine e_saxs.

The dimension is presently 2,000 residues; to change this, change the statement parameter (maxres=xxxxx) in the DIMENSIONS file in all source directories.
The archives contain the following:

src-HCD-5D_nmr-SAXS-Xlink-2021-07-07.tar.gz UNRES source code
wham-src-HCD_nmr-SAXS-2021-07-07.tar.gz wham source code
cluster-src-HCD-nmr-SAXS-2021-07-07.tar.gz cluster source code
PARAM-2021-07-07.tar.gz parameter files
example.tar.gz example of crosslink-assisted MD simulations

You can download this version of UNRES in the downloads section.