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maccallumlab / meld

Modeling with limited data
http://meldmd.org
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building system from amber files #145

Open doesm opened 1 year ago

doesm commented 1 year ago

Hi,

I'd like to build an explicit solvent model from amber files.

According to the tutorial in https://github.com/maccallumlab/meld/blob/master/docs/how_to/explicit_solvent.rst : s = system.builder.load_amber_system('system.top', 'system.crd')

Is this option still available?

Regards,

Marcelo.

jlmaccal commented 1 year ago

That particular method got lost in some previous code refactoring. We could probably add back similar functionality.

alberto99 commented 1 year ago

I think that would be a good idea. Otherwise we should figure out good equilibration protocols to use after solvating the system in openmm.

On Mon, Mar 13, 2023, 6:46 PM Justin MacCallum @.***> wrote:

That particular method got lost in some previous code refactoring. We could probably add back similar functionality.

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doesm commented 1 year ago

yes, that would be great!

jcr13 commented 12 months ago

I'm interested in this too. I want to run peptides that have non-natural amino acids and was thinking I could parameterize in antechamber and save the amber prmtop and crds to load into MELD.

emiacetale commented 11 months ago

Hi everyone, This would be very useful! I might be thick, but I can't think of a current route to use nonstandard amino acids or do relative binding affinities of drugs.

jcr13 commented 11 months ago

I am interested in looking at systems like ones in this paper and assessing how changes in peptide sequence (especially with nonstandard amino acids) impact free conformation of the peptide, and separately peptide-ligand binding. I grabbed this system just as an example, so not too familiar with the details but often there's NMR data that can be used as restraints for systems like this.