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Biomolecular Reaction & Interaction Dynamics Global Environment
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BRIDGE Not on https://cheminformatics.usegalaxy.eu/ #1

Open christos-efthymiou opened 2 years ago

christos-efthymiou commented 2 years ago

Hi,

I would like to follow the NAMD tutorial https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/md-simulation-namd/tutorial.html and it mentions that NAMD is not on Galaxy so it is necessary to download NAMD yourself. When I get to this Github page, it says:

"In collaboration with Björn Grüning and the Galaxy computational chemistry team, these tools are available on Galaxy Europe under the Chemical Toolbox section."

However, when I visit https://cheminformatics.usegalaxy.eu/, BRIDGE is not under the Chemical Toolbox section. Can you please explain how to access BRIDGE on Galaxy to be able to follow the above tutorial?

tsenapathi commented 2 years ago

Dear @christos-efthymiou

Thank you for your interest in using the BRIDGE. The NAMD tools are not in the Galaxy Europe server due to some technical difficulties. NAMD is open-source, however, you need to register and download it from their webpage. Due to this reason, we cannot make the auto-install using the conda package.

You can use NAMD tools using docker containers, but you will need to build the tools and download NAMD and install manually. If you want to do that, I can assist.

Simon has built some amazing opensource tools to do MD simulations using GROMACS and they are freely available in the Galaxy Europe server. If it is possible use them instead.

Hope this helps! Tharindu

christos-efthymiou commented 2 years ago

Dear Tharindu,

I have downloaded VMD and NAMD to my local computer, but the simulations are too computationally intensive to run on my computer. Therefore, I was hoping to be able to create the setup files using QwikMD, and then upload all files necessary to run the simulation on Galaxy. Is this possible with the Docker containers? I am still new to this process so I apologize for my limited understanding.

I would also be happy to use GROMACS, but I have tried following the GROMACS tutorials and they do not work for my system of interest. I would like to run a MD simulation of PDB file 2XQW, which contains 3 protein chains. Are there any published workflows or tutorials which describe how to use GROMACS on Galaxy to run simulations of protein-protein complexes?

I greatly appreciate any help you can provide.

Best, Christos

On Tue, Mar 8, 2022 at 8:32 PM Tharindu Senapathi @.***> wrote:

Dear @christos-efthymiou https://github.com/christos-efthymiou

Thank you for your interest in using the BRIDGE. The NAMD tools are not in the Galaxy Europe server due to some technical difficulties. NAMD is open-source, however, you need to register and download it from their webpage. Due to this reason, we cannot make the auto-install using the conda package.

You can use NAMD tools using docker containers, but you will need to build the tools and download NAMD and install manually. If you want to do that, I can assist.

Simon has built some amazing opensource tools to do MD simulations using GROMACS and they are freely available in the Galaxy Europe server. If it is possible use them instead.

Hope this helps! Tharindu

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