Generate unfolded topology from FASTA sequence

I’m looking to run some simulations of the folding process for some small proteins. What’s the “best practice” method of converting a FASTA sequence into an unfolded structure? What rules-of-thumb should I use for the box sizing? I would assume there would be tools/scripts that do this automatically, possibly already in GROMACS, but I can’t find anything via DDG or the reference documentation.

GROMACS does not have any ability to construct coordinates from sequences (or anything else, honestly). It only has limited support for building missing H atoms.

Thanks for the confirmation. For anyone reading this in the future and wondering what I ended up doing: I used the “Protein Builder” dialog from VMD’s Molefacture plugin. editconf (GROMACS) then sizes the box (or 3D polygon) based on a given keep-out distance.

Hi there,
You actually can use tleap from AMBERTools (which is free) to generate the coordinates.
Then you can easily convert to GROMACS run files by calling