7. COBRAMM
Overview
Teaching: min
Exercises: minQuestions
Objectives
Table of Content
1. Theory and Hands on with COBRAMM
1.1. Slides
1.2. Videorecording of the session
Afternoon, July 6 section
- Zoom recording
- Webcast
Morning, July 7 section
- Zoom recording
- Webcast
Afternoon, July 8 section
1.3. Demonstrations and Handson
1.4. Instructions 1
1. Add these variables to your .bashrc file
export COBRAM_PATH=/projects/academic/cyberwksp21/Software/cobramm
export AMBERHOME=/projects/academic/cyberwksp21/Software/Conda/Miniconda3/envs/ambertools22/
export PATH=$AMBERHOME/bin:$PATH
export PATH=$COBRAM_PATH/cobramm:$PATH
export PATH=$COBRAM_PATH/util:$PATH
And load it
source .bashrc
2. Load modules and activate environment
module load openbabel
conda active ambertools22
3. Get the initial files
git clone https://github.com/compchem-cybertraining/Tutorials_COBRAMM.git
cd Tutorials_COBRAMM/COBRAMM/solvated_preparation
[](../fig/cobramm/prepare_cobramm_input.png)
4. Solvation
python $COBRAM_PATH/util/cobramm-solvatedchromo.py -xyz trans_azobenzene.xyz --solvent methanol -sz 15
[](../fig/cobramm/solvate.png)
5. Equilibration
python $COBRAM_PATH/util/cobramm-equilibration.py -p trans_azobenzene.top -c trans_azobenzene.crd -opt 10 -ht 1 -et 1
[](../fig/cobramm/equilibration.png)
6. Droplet
python $COBRAM_PATH/util/cobramm-droplet.py -p trans_azobenzene.top -c finalsnapshot.crd -sr 12 -mr 4
[](../fig/cobramm/droplet.png)
1. Link atom example
1. Go to:
cd Tutorials_COBRAMM/COBRAMM/Rh_preparation/input
2. Run
./Prepare_cobramm_input.pl
1.4. Homeworks
Key Points