SuAVE 2.0.0

DESCRIPTION:

The Surface Assessment Via grid Evaluation (SuAVE) software was developed to account for the effect of curvature in the calculations of structural properties of chemical interfaces regardless of the chemical composition, asymmetry, and level of atom coarseness. It employs differential geometry techniques, enabling the representation of chemical surfaces as fully differentiable.

Denys E. S. Santos wrote the code and conceived the algorithm and mathematical formalism. Thereza A. Soares conceived the idea and supervised code development, and Kaline Coutinho revised the code and provided expertise with the equations and discussion.

CITATION:

Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape. (2022) Denys E. S. Santos, Kaline Coutinho, Thereza A. Soares. J. Chem. Inf. Model., v. 62, p. 4690–4701.

SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces (2020) Denys E. S. Santos, Frederico J. S. Pontes, Roberto D. Lins, Kaline Coutinho, Thereza A. Soares. J. Chem. Inf. Model., v. 60(2), p. 473-484.

INSTALLATION:

SuAVE can be compiled in any operational system, is distributed free of charge and it is maintained by a single developer. If you experience code issues, we kindly request you to contact us at e-mail: suave.biomat@gmail.com

Prerequisites for installation:

-> cmake installed

-> gfortran installed

-> library libquadmath installed

In order to install the programs and enjoy your analysis time, please follow the steps below:

1- Download the code:

-> From GitHub web Page clone the repository through the following commmand:

   git clone https://github.com/SuAVE-Software/source.git

-> Dowload the compiled version from SuAVE Web Page

2- Compile the source code:

If you downloaded the compiled version you just need to insert the files on a convenient path in order to be run. If you downloaded the source code, please compile it by the use of any FORTRAN compiler and the MakeFile.

->> Enter the directory where you have downloaded the code

   cd ~/PATH_TO_SRC/

->> Uncompress XTC library and install it!

    unzip library.zip.
   ./install_lib.sh
    sudo ldconfig

->> Edit makefile in order to proceed with the installation process. Edit INSTALL_PATH content to update the PATH where you want to place the compiled source, and also the FCFLAGS to adapt it to your needs.

   FCFLAGS = -O2 (DEFAULT)
   INSTALL_PATH = /usr/local/suave (DEFAULT)

(The use of flags -O2 or -O3 is well accepted by this compiler and the code. It will be helpful for extracting the best performance of SuAVE) (SuAVE version 2.0.0 is also able to use OpenMP parallelization. To do so, the user has to insert the flag -fopenmp on FCFLAGS directive)

->> Once with the makefile updated, run make!

   make

   sudo make install

->> Insert the following directives in the .bash_profile file:

   export SUAVE=/usr/local/suave
   export PATH=$SUAVE:$PATH

->> Update the bash

   source .bash_profile

or

   source .bashrc

->> Have fun with your analysis !

USAGE:

A classical use for most of SuAVE tools is exemplified below for s_densph:

Usage: s_densph -in file.pdb -ind1 file1.ndx -ind2 file2.ndx -dens dens.ndx

file.pdb ---- atomic coordinates in PDB format

file.ndx ---- index file containing user-selected atoms used to fit the grid points to the chemical surface.

dens.ndx ---- index file containing user-selected atoms used to calculate density profile.

Options:

-bin defines the number of rectangular partition bins along the phi- and psi-angles

-grid generates a PDB file containing the grid points used in the fitting for the last frame in the trajectory file.

-rmsd calculates the RMSD between the fitted grid and the selected atoms in the index files. This estimates how precisely is the grid surface fitted to the chemical surface throughout the trajectory file.

-coarse generates a coarse grid over the surface index atoms from which a finer grid will be generated. This is recommended for surfaces defined by atoms which greatly fluctuate throughout the trajectory.

-begin first frame to use in the calculations

-end last frame to use in the calculations

-skip number of trajectory frames to be skipped during the analysis

-slices defines the number of slices along the axis normal to the system used to calculate the density profile

-rough percentage of the original surface roughness the user wants to keep (1.0 by default, meaning 100%)

-help prints HELP information and quits

For more information as to the usage of each code, please use -help flag, or see the Tutorial on SuAVE Web page