CLI Overview

MartiniSurf exposes one main command with module entrypoints. This page is the quick navigation map for the CLI. The detailed flag-by-flag reference lives in MartiniSurf Quick Guide for New Users.

Compact package help

martinisurf -h

Full package help

martinisurf --full-help

Main pipeline help

martinisurf build -h

This is the main detailed help page for end-to-end system construction.

You can also call build flags directly without build:

martinisurf --pdb 1RJW --moltype Protein --surface-mode 4-1 --lx 15 --ly 15 --anchor B 8 10 11

For --pdb workflows, --anchor and --linker-group accept either legacy global residue ids or chain-based residue ids from the input PDB. In --complex-config workflows, low-Z balancing is enabled by default (protein.balance_low_z=true, default fraction 0.2).

Adsorption mode (--ads-mode)

--ads-mode is an anchor-based adsorption workflow:

  • Keeps classical anchor orientation behavior.

  • Skips anchor pull/restraint topology generation.

  • Generates MDP stages for minimization, nvt, npt, and production (no deposition stage).

  • Is incompatible with linker mode (--linker / --use-linker).

Module helps

martinisurf surface -h
martinisurf orient -h
martinisurf system -h

For complete flag-by-flag details, see MartiniSurf Quick Guide for New Users.