building system from amber files

[doesm]

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]

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

[alberto99]

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]

yes, that would be great!

[jcr13]

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]

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]

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.