lbsymt-developers / vinaprocess

Automatized Docking Algorithm

VinaProcess

Automatized Docking Algorithm

Dependences

• Linux OS
• Perl
• Python

Installation

Extract file vinaprocess-0.04.tgz

gunzip /Directory/of/the/vinaprocess/home/vinaprocess-0.04.tgz
tar -vxf /Directory/of/the/vinaprocess/home/vinaprocess-0.04.tar

Usage

set variable VINAPROCESS to the root of the extracted directory

export VINAPROCESS=/Directory/of/the/vinaprocess/home

To run on a single thread:

$VINAPROCESS/vina-process.pl -r receptor.pdb -l ligand.pdb 

Notes:

In a directory with the ligand and receptor in pdb format file,

the program will create a directory of the format YYYYMMDDHHMM from the date.

Inside, you will obtain the resulting compound in format of "energy-receptor-lingand-X-Y-Z".

It's not obligatory to have the 2 files of compound inside the directory of work.

For more help:

$VINAPROCESS/vina-process.pl -h

Options:

-r : Receptor file (pdb format)

-l : Ligand file (pdb format)

-c : Cores number (by default 1)

-h : help

Developers

• M. en MM. Nidia Beltrán Hernández 1
• M. en C. Jerome Verleyen 2
• Dr. Fidel Alejandro Sánchez Flores 2
• Dr. Heriberto Manuel Rivera 1

1 Laboratorio Biología de Sistemas y Medicina Translacional, Facultad de Nutrición-Universidad Autónoma del Estado de Morelos. 2 Unidad Universitaria de Secuenciación Masiva y Apoyo Bioinformático, Instituto de Biotecnología-Universidad Nacional Autónoma de México

vinaprocess's Issues

pdbqt file conversion error

Hello I got

Conversion of receptor -> pdbqt file ..: Error in converting receptor (rec.pdb) -> pdbqt file : 32512

Are there formating requirements for the pdb file? Thanks!