Commands

The following commands are defined by the pmlbeta plugin:

α/β-peptide Construction and Manipulation

betafab2

build a beta-peptide

fold_bp

fold a beta-peptide into the desired secondary structure

select_bbb

select the beta-backbone

Residue Topology Recognition

renumber_peptide_chain

recognize and mark residues in a peptide chain

residue_topology_candidates

find matching building block topologies from a GROMACS residue topology database file

assign_residue_topology

assign atom properties from a matching building block topology

Input / Output

save_crd

output to the extended CHARMM CRD format

save_gro

output to the GRO format of GROMACS

save_g96

output to the G96 format used by GROMOS and GROMACS

Secondary structure database manipulation

ssdb_add

add/edit an entry

ssdb_del

remove an entry

ssdb_list

list the entries

ssdb_dihedrals

get the dihedral angles corresponding to an entry

ssdb_resetdefaults

reset the secondary structure database to its default state

Miscellaneous

gmx_beta_backbone_dihedrals_selection

create selection files for beta-peptide backbone dihedrals, understandabe by GROMACS