Dear all, Due to the size of the molecule I am studying (> 200 atoms) the LigParGen web server can not be of help.
I am a chemical engineer but I have very little experience in instaation of softwares.
I know that yhe aq.m. package can be installed on a local computer, but I wasn't able to find a detailed guideline.
Could somebody help me?
Thanks
Paolo
p.s. my PC runs on windows
Dear Dr. Paolo Botto,
Here it is:
LigParGen v2.1
Author: Israel Cabeza de Vaca Lopez Email: [email protected] // [email protected] Place: William L. Jorgensen Lab at Yale University // Jens Carlsson Lab at Uppsala university Date: 2020-2021
Description: An automatic OPLS-AA parameter generator for small organic molecules using CM1A, 1.14CM1A and CM1A-LBCC charge models. LigParGen accepts any Open Babel molecular format including SMILES, PDB, MOL, MOL2, among others. Final OPLSAA parameter outputs will be written in topology/coordinate input files for BOSS, Q, Tinker, PQR, openMM, CHARMM/NAMD, Gromacs, LAMMPS, Desmond, and xplor softwares.
Note: This new version has been written from scratch but it is based on the Leela Dodda initial ligpargen python code.
WARNING: This version of ligpargen requires BOSS5.0 to work correctly. Some features like CM1A-LBCC are not available with the BOSS version provided by the Jorgensen Lab website. I strongly recommend you request a BOSS5.0 executable by sending an email directly to Prof. Jorgensen ([email protected])
New LigParGen features:
- The order and the name of the atoms will remain the same in the output files.
- This new version of the ligpargen includes a robust version of the alchemical transformation method to generate single and dual topologies for four different molecular mechanics softwares (BOSS, CHARMM/NAMD, Gromacs, and Tinker).
- Sanity checks to detect incorrect inputs have been implemented (incompatible charge model, net molecule charge, input format, ...).
- A log file to check the inputs, outputs, and intermediate processes has been created. This allows tracking the input information (charge model used, input molecule,...) and also provides useful warnings in case of error.
- Automatic net charge detection in the input molecule. If the user specifies a different charge than one automatically estimated, the log file will include a warnning.
- Atom XYZ positions in the molecule input remain unchanged in the output files.
- Hydrogen atoms will be added automatically just for SMILES inputs. Molecules in any other input format require to have all hydrogens to provide more flexibility of the protonation states. In this way, the user can avoid parameterization problems with tautomers or stereoisomers.
- Different molecule input format, net charges, charge models, and optimization steps can be used for each molecule in alchemical transformations.
- Bugs fixed (Q wrong torsion parameters, alchemical molecule overlap failure,...)
- Additional default input parameters have been included such as residue name, charge model,...
INSTALATION
LigParGen requires the free BOSS software to generate the OPLSAA parameters.
1 - Download and install BOSS software from the official William L. Jorgensen lab website: http://zarbi.chem.yale.edu/software.html
BOSS is compiled for linux using 32 bits libraries so it can not run in windows using WSL. Alternatively, you can use a virtual machine in windows such as virtualBox to install a linux distro (ubuntu, centos, ...) and run LigParGen.
1.1 - Set the BOSSdir enviromental variable:
- bashrcexport BOSSdir=PATH_TO_BOSS_DIRECTORY
- cshrcsetenv BOSSdir PATH_TO_BOSS_DIRECTORY TIP: add this command line in your ~/.bashrc or ~/.cshrc file.
2 - Download and install conda (anaconda or minicoda):
wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh
or
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
3 - Create and activate an enviroment for python3.7 (Everything was tested with 3.7):
conda create --name py37 python=3.7 conda activate py37
Optional TIP: add this line to your .bashrc/.cshrc,....
4- Install rdkit and openbabel in py37 enviroment
conda install -c rdkit rdkit conda install -c conda-forge openbabel
5 - Download and install LigParGen
git clone https://github.com/Isra3l/ligpargen.git pip install -e ligpargen
Optional: Check your installation by runing the tests included in the ligpargen folder.
cd ligpargen;python -m unittest test_ligpargen/test_ligpargen.py
TIP: Do not forget to activate your py37 enviroment before using LigParGen.
conda activate py37
https://github.com/Isra3l/ligpargen?ysclid=lcov6g244u769334903
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Please follow the below steps to have a local version of LigParGen
Dear Satish, thanks a lot. Let me apologize for being very "green" in this field, so I have some questions that I hope you may kindly answer:
1) My machine runs with Windows. Would it be necessary to install first a Linux "virtual machine" and, is so, how?
2) Ref. to your point 4, what does it mean "here"? I actually already downloaded the LigParGen2 folders. They are: LigParGen and Lig.ParGen.egg-info, plus two additional files, setup.cfg and setup.py. Are these the ones you are referring to? Should I copy all of them?
Thanks again
Paolo
Hello!
Does anybody know what the license for the BOSS software is? Asking since I'm an industrial researcher and I need to know if I'm allowed to use BOSS for my purposes.
Secondly, BOSS v 5.0. isn't easy to get, since Prof. Jorgensen simply doesn't reply to the email. Is there another way to get it?
Many thanks in advance!
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