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Published 20 hours ago • verified publisher icon marrink-lab

ssDNA Tutorial: Broken Link

Open jan-stevens opened this issue 2 years ago • 2 comments

As the name suggest, there is a broken link in the Single stranded circular DNA tutorial. We use the amber14-parmbsc1 force field, which are no long online available from "official" sources due to the GROMACS Force Fields: User contributions web-page being offline. The broken link makes it difficult for users to complete the tutorial.

A possible solution would be supporting the amber14sb-OL15 force field. The OL15 version is recommended by the amber developers for DNA simulations and a GROMACS port is provided by the authors here.

Cheers, Jan

jan-stevens avatar May 24 '22 12:05 jan-stevens

I think that is a good idea. Do you feel up for giving it a try to implement these parameters or shall I? Also the polyply regression tests has the force-field files as a copy so for now we can fix the link

fgrunewald avatar May 30 '22 09:05 fgrunewald

For now I fixed the link but again implementing this recommended FF is good practice anyways

fgrunewald avatar May 30 '22 09:05 fgrunewald