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License: GNU General Public License v3.0
Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark This repository includes scripts to back-calculate NOEs from biomolecular ensembles, such as the ones obtained by a MD simulation, as well as to compare to a set of experimental ones. It contains two python scripts: 1. NOEconverter.py which helps in the creation of the right file format for the experimental data 2. g_reff to carry out the calculation of NOEs from the ensemble, as well as to compare with the experimental NOEs. usage: g_reff [-h] -r NOES [-p PDB] Calculate Reff on selected atom classes from an MD simulation optional arguments: -h, --help show this help message and exit -r NOES, --reff NOES noes file -p PDB, --pdb PDB pdb file EXAMPLE An example is provided in this repository with a short trajectory to test the tool. The first step is the conversion to the proper NOE format using as input: i) the first frame of the ensemble, for example First_frame_chain_A.pdb, as a reference pdb file; ii) the file with the experimental NOEs from the BMRB database; iii) a conversion table for the atom name compatible with the force field used in the simulation (in the example CHARMM) python NOEconverter.py -pdb First_frame_chain_A.pdb -noe BMRB_NOE.mr -c AAtable_new_CHARMM.par This step generates a .dat file that can be used by g_reff The second step is the calculation of the NOEs from the ensemble and its comparison with the experimental data python2.7 g_reff -r NOE_converted.dat -p trajectory.pdb When using the g_reff and NOEconverter.py for publication please cite: Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth, Juan Salamanca Viloria, Emmanuelle Bignon, Elena Papaleo*, Analyzing biomolecular ensembles, Methods Mol Biol. 2019;2022:415-451. doi: 10.1007/978-1-4939-9608-7_18.
dear all just so we know,
the example in the repo is not working with me. I would like another person to try to clone it and run it.
I revised the README according to my understanding of the tools and put the files for the example in a separate folder.
I run first
python NOEconverter.py -pdb First_frame_chain_A.pdb -noe BMRB_NOE.mr -c AAtable_new_CHARMM.par
and this worked smoothly
then
python NOEconverter.py -pdb First_frame_chain_A.pdb -noe BMRB_NOE.mr -c AAtable_new_CHARMM.par
and this doesn't work returning:
Traceback (most recent call last):
File "g_reff", line 121, in
gro = args.gro
AttributeError: 'Namespace' object has no attribute 'gro'
but there is no gro file in the help/example even if I recall that the first version of this script was using gro file as well...
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