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CG2AA:
Backmapping Protein Coarse-Grained Structures
L. E. Lombardi (IC/DM) - M. A. Martí (IQUIBICEN/DQB) - L. Capece (INQUIMAE/DQIAQF)

Coarse-grained models allow long-scale simulations with a much lower computational cost than that of all-atom simulations. However, the absence of atomistic detail impedes the analysis of specific atomic interactions that are determinant in most interesting processes in biomolecules. In order to study these phenomena, it is necessary to reconstruct the atomistic structure from the coarse-grained representation. This structure can be analyzed by itself or be used as an onset for atomistic molecular dynamics simulations. Here we present an algorithm that accurately reconstructs the atomistic structure from coarse-grained models from the force field developed by Hills, Lu and Voth , using a simple geometrical algorithm.



Download

The software, wich consists in a python script, is freely available here: cg2aa.py. It requires the NumPy library. It is likely you have already everything installed for cg2aa to run. If not, in Ubuntu or Debian, for example
apt-get install python2.7 python-numpy
should do the trick. For more information and installation guide for the requiered software, please visit Python 2.7 and NumPy.

Tutorial

In order to run the program, you need a PDB file with your protein structure in the Coarse Grained representation. The name of this structure should end in 'cg.pdb'. Now, to convert a file named 'NAMEcg.pdb', type:
/path_to_script/cg2aa.py path_to_file/NAME
For example, if the current directory holds not only the script but the file to process, just type:
./cg2aa.py NAME
The output will be an all-atom pdb file named 'NAMEbm.pdb'.

Please, note that you can provide a reference all-atom pdb file to recall histidine information by placing a file named NAME.pdb in the same folder. In that case, histidines are going to be labeled as HIE, HID or HIP as in the original all atom pdb. If the reference pdb is not present, all histidines will be named HIS.

The reference structure can be used to get a root mean squared deviation report (of the backmapped structure with respect to the original one) by adding the -rmsd flag:
./cg2aa.py -rmsd NAME 

A modest help is available via the -h or --help flags:
./cg2aa.py --help

Example: Myoglobin (PDB entry 1VXD)

Start with the coarse grain file Mbcg.pdb. From the comand line, type
path_to_script/cg2aa.py path_to_file/Mb
For instance, if both the script and the file are in the current directory, type:
./cg2aa.py Mb
You sould get a file named Mbbm.pdb. If you want, you can provide a reference Mb.pdb for histidine labeling. In that case, the output should look like this. Here, you can visualize the results of this process: the original all atom pdb in green and in cyan the output of backmapping the coarse grain structure.

Visualization of the CG model

We provide a script: tcl-gen.py that generates a structure-specific tcl code to run inside VMD in order to present a custom visualization. Its usage is simple, from a command line just type:
./tcl-gen.py CGFILE.pdb
An it will produce a tcl script named CGFILE.tcl. For the example above, for instance, the command
./tcl-gen.py Mbcg.pdb
should produce a file Mbcg.tcl
 
 
 
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