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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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Problem with the AMBER builder #1028

Closed jnoske closed 2 years ago

jnoske commented 2 years ago

Hello, I have problem with the builder in htmd 2.0.3. I want to build a protein-ligand-system. Previously in the tleap input file, the ligand was loaded as a .mol2 file and combined with the protein. Now the protein and the ligand are in one .pdb file and tleap crashes because there are no parameters for the residue:

FATAL: Atom .R<MOL 204>.A<H8 21> does not have a type.

The .frcmod parameters are loaded as well, so I dont unterstand why it cannot provide parameters for my ligand, previously when my ligand was loaded as mol2 file and combined in tleap everthing worked fine.

input.txt param0_ligand.txt tleap.txt

stefdoerr commented 2 years ago

Hi, the building behaviour indeed changed in the last HTMD versions. You now need to pass also the prepi or mol2 file in amber.build topos argument like this and the filenames need to match between the frcmod and prepi/mol2. I definitely need to add documentation on this though, I had totally forgotten.

        params = amber.defaultParam() + [os.path.join(refdir, "BEN.frcmod")]
        topos = amber.defaultTopo() + [os.path.join(refdir, "BEN.mol2")]

        bmol = build(newmol, outdir=tmpdir, param=params, topo=topos, ionize=False)
jnoske commented 2 years ago

Thanks that works!

stefdoerr commented 2 years ago

I updated now the tutorial on github and will be available on the next release. Thanks for the report!