CHARMM force-field customizations

Pestifer bundles a CHARMM force field for each supported release under pestifer/resources/charmmff/<release>/ (currently feb26). The bundled toppar tarball is trimmed to the files pestifer actually loads — the top-level topology/parameter/stream files plus the stream/ subtree — via scripts/trim_toppar.sh; the upstream subdirectories pestifer never reads (metals/, drude/, non_charmm/, implicit-solvent sets, etc.) are dropped. Beyond the stock CHARMM toppar files, there are two kinds of local additions:

  • <release>/patches/ — records of corrections applied by hand to specific upstream toppar files. These live per release, since each patch targets a particular release’s toppar file.

  • custom/ — extra topology / parameter / stream files that are not part of the base CHARMM release. These are release-independent, so they live in a single shared charmmff/custom/ directory that is a sibling of the release directories (not duplicated under each one).

Note

The .patch files under patches/ are provenance only — nothing in pestifer applies them at build or package-regeneration time. The corresponding upstream .str file shipped in the release already contains the fix; the .patch is kept so the exact change (and the reason for it) is recoverable.

Corrections to upstream files (patches/)

toppar_all36_lipid_cardiolipin.patch

Corrects internal-coordinate (IC) table entries for cardiolipin acyl-chain hydrogens. For the second hydrogen of several methylene pairs (H12A/H12B and H13A/H13B on both the A- and C-chains), the released file repeats the previous IC line’s leading atom instead of naming the partner hydrogen — e.g. IC CA13 CA11 *CA12 H12B where it should read IC H12A CA11 *CA12 H12B. With the wrong leading atom, guesscoord builds the two hydrogens of the pair at the same position. The patch sets the correct leading atom so each hydrogen is placed distinctly.

toppar_all36_prot_modify_res.patch

Corrects the coordinating nitrogen in the two histidine–zinc covalent-link patches. By name and intent, ZNHD bonds the zinc to a histidine’s delta-1 nitrogen (ND1) and ZNHE to its epsilon-2 nitrogen (NE2). The released file has the two bonds swapped (ZNHD → NE2, ZNHE → ND1); pestifer’s copy restores them so each patch links the zinc through the nitrogen it is named for. These patches are used in the insulin-hexamer example build (Example 13), whose zinc ions are coordinated by histidines.

Added definitions (custom/)

These files supply residues, patches, parameters, and ions not present in the base CHARMM release. They live in the shared charmmff/custom/ directory and are loaded alongside the stock toppar for whichever release is active.

pestifer.top

A small topology file of pestifer-specific patches:

  • a patch converting a standard up-puckered proline to a down-puckered proline (PROD);

  • several terminus-“undoing” patches (to reverse standard N-/C-terminal patching);

  • a deprotonated tyrosine.

toppar_all36_moreions.str

Additional monatomic-ion definitions, taken from CGenFF.

vcg-paramchem-ic.str

A CGenFF/ParamChem stream file for Polysorbate-80 (RESI VCG), including the internal coordinates needed to build it.

83G-cgenff.str

CGenFF/ParamChem parameters for ligand 83G — the HIV-1 entry inhibitor BMS-378806, present in the HIV-1 Env ectodomain examples (see Examples 9 and 10).

LF0-cgenff.str

CGenFF/ParamChem parameters for ligand LF0 — an HIV-1 integrase inhibitor (see PDB entries 4ID1, 4LH5, 4TSX, 8A1P, 8USY, 8V0Z).

Contributing new custom definitions

The 83G and LF0 streams are examples of built-in custom residue definitions. To add your own from any file containing a CHARMM RESI block (a .str, .rtf, or .top file), use modify-package — see modify-package — which installs it into the shared charmmff/custom/ directory and records the change in the modifications ledger.