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galaxycomputationalchemistry / galaxy-tools-compchem

:mega: Galaxy Tools for Computational Chemistry
Apache License 2.0
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added a new tool to convert file from AMBER to GROMACS #142

Closed thepineapplepirate closed 2 years ago

thepineapplepirate commented 2 years ago

This tool uses one of acpype's functionalities, where it can take any AMBER topology and coordinate files, and convert them to GROMACS files ready for simulation. Currently, this function of acpype can fully convert a solvated system with TIP3P water. The developers are working on extending this versatility to the other water models as well. At any rate, unsolvated systems can also be converted and then solvated later in GROMACS.

This tool will be useful because there are many specialized force fields that are not in GROMACS (such as metal binding site force fields like ZAFF), but acpype will convert them over successfully, even if they cannot be loaded in gromacs initial setup. I'm also adding the test files in the test-data/ folder. They are helicase_complex_solv.prmtp/inpcrd. Cheers!

simonbray commented 2 years ago

Can you make the test data smaller please? It gets packaged along with the tool, so ideally should not be more than a few kb.

Otherwise this looks great to me.

thepineapplepirate commented 2 years ago

Can you make the test data smaller please? It gets packaged along with the tool, so ideally should not be more than a few kb.

Otherwise this looks great to me.

That should be no problem. I will go ahead and make a smaller test set. Thanks!

simonbray commented 2 years ago

Thanks!