SOLVATE(1)

📦 version 1.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💧 SOLVATE(1) — the one where your protein gets a whole water moment

okay bestie, listen up, because this is literally solvate, a general commands manual page, and it's about to give your solute the hydration era it deserves 🫶

✨ NAME ✨

solvate — surround protein with water molecules 🌊

no fr, that's the whole job. your protein's been out here dry and crusty and solvate shows up like "not on my watch" 💅

🌸 SYNOPSIS 🌸

solvate [-tthick][-rradius][-nngauss][-ug][-ub]
               [-s] [-v] [-bulk] [-w] [-ion] [-psf] [infile] outfile

the way this is just a lil parade of flags followed by files… iconic honestly 👑

🦋 DESCRIPTION 🦋

SOLVATE prepares a water shell around solutes. that's it, that's the vibe — it builds the hydration layer, the lil aqueous aura, the aquatic fit check ✨

solvate command. 🎀

💖 OPTIONS 💖

here's the whole rundown of the options, and yes, we're going through every single one because nothing gets skipped in this house 💜

  • -t thick — minimum water shell thickness in Angstrom (default: 10.0). think of it as "how thick do we want the water coat to be, bestie" 🧥
  • -r radius — maximum boundary curvature radius in Angstrom (default: 100000.0). big number, big radius, no cap 🌈
  • -n ngauss — use ngauss gaussians to define solvant boundary (default: 1). yep, gaussians, plural, as many as you want 💀
  • -s — write surface statistics to file surface_stat. receipts! 📝
  • -v — write volume statistics to file volume_stat. more receipts! 📊
  • -ug — use gaussians from file gaussians (skip gaussian learning phase). skipping class, but make it legal 🙈
  • -ub — use boundary definition from file boundary (skip gaussian learning phase and boundary adjustment). it's giving "we already know what we're doing" 💅
  • -bulk — output only bulk water (i.e., no buried water molecules). surface-level friendships only, periodt ✋
  • -w — output only water molecules (i.e., not the solute). bye solute, this is water's moment 👑
  • -ion — add ions (na+/cl-) in isotonic/Debye-Hueckel concentration. salty behavior, literally 🧂
  • -psf — output XPLOR-script mkpsf.inp for generating a psf-file. script drop, slay 💾
  • infile — pdb-file (no extension) of solute (if omitted, a water droplet is created). no solute? no problem, we just make a whole droplet 🫧
  • outfile — pdb-file (no extension) of water shell. the final product, the glow-up, the reveal ✨
heads up bestie: infile is optional, but outfile is not. one of them has main character energy and it's the one that must be there 💅

🔥 SEE ALSO 🔥

(no references listed here, bestie — the page just leaves this one empty, which is its own kind of mysterious 🎀)

🌟 AUTHOR 🌟

SOLVATE was written 1996 by Helmut Grubmueller. a legend, fr fr 🫶

This manual page was written by Steffen Moeller <moeller@debian.org>, for the Debian project (but may be used by others). shoutout, that's so generous of them 💖

aaaand that's the whole page!! this one came from the Debian General Commands Manual, page SOLVATE(1), dated Dezember 28, 2007 🌸 drink some water (ironic, I know) and hydrate your own lil shell 🦋💧

📦 where this page comes from