xplor2gmx(1)

💖 NAME 💖

xplor2gmx — bestie, it converts XPLOR distance restraints into GROMACS format. That's the whole job. She's a specialist. 🎀

✨ SYNOPSIS ✨

xplor2gmx (residue offset)  input.pdb

no cap, that's the shape of it — offset first, then the pdb file. 🦋

🌸 DESCRIPTION 🌸

okay so here's the tea. xplor2gmx reads an XPLOR input file that's got distance restraint data in it — the kind of thing you sometimes find just vibing in the pdb database (http://www.pdb.org). 🫶

heads up bestie: before you run this, the dihedral restraints should be removed from that input file, so that only the distance restraints are left. She only wants the distance ones. 💅

She can also handle ambiguous restraints, which is lowkey iconic of her. Then she converts all those distance restraints into GROMACS format. slay. 👑

So the flow is: a restraints file (.dat) comes in on STDIN, and a suitable output file (.itp) goes out on STDOUT. Pipes are the moment, fr fr. 🌈

🍓 EXAMPLES 🍓

xplor2gmx.pl 33 conf.pdb < restraints.dat > disre.itp

look at her go — restraints in, itp out, zero drama. ✨

💅 OPTIONS 💅

xplor2gmx requires two command line options, no more no less, she's not flexible like that:

• the residue offset (an integer) — first one up, bestie. 🔢
• the .pdb filename — second one. 🗂️

⚠️ real talk: the pdb file must have correct atom numbers. If the atom numbers are lying to you, that's a whole different problem and this script is not the one to fix it. 😭

🔥 SEE ALSO 🔥

• gromacs(7) — go read that one too, iykyk. 💜

k that's the whole page!! sending u love from the GROMACS suite, Version 4.0, dated 13 Oct 2008 — yeah she's vintage, she's a classic, she ate and left no crumbs, periodt. 💖🧚⭐