Build peptide#

Building peptides from amino acid sequence.

Peptides are essential building blocks in molecular modeling. The function molsysmt.build.build_peptide() constructs an all-atom molecular system with topology and coordinates directly from an amino acid sequence, supporting three-letter or single-letter codes and terminal cappings specified in the sequence. It uses MolSysMT’s native engine by default; pass engine='LEaP' to use the optional AmberTools executable. Both sequence notations work without Biopython.

Added in version 1.0.0.

API documentation

Follow this link for a detailed description of the input arguments, raised errors, and returned objects of this function: molsysmt.build.build_peptide().

Basic usage#

Let’s show how to build a capped dipeptide (AceAlaNme) from sequence:

import molsysmt as msm

molsys = msm.build.build_peptide('AceAlaNme')

msm.view(molsys)

Next, let’s build a longer cationic peptide sequence (GRKFRRKFKK) and solvate it in a simulation box:

molsys = msm.build.build_peptide('GRKFRRKFKK')

We cap the terminal residues with ACE and NME:

molsys = msm.build.add_missing_terminal_cappings(molsys, N_terminal='ACE', C_terminal='NME')

Center the peptide in space before solvation:

molsys = msm.structure.center(molsys)

Solvate the system in a truncated octahedral box with 14.0 Å clearance:

molsys = msm.build.solvate(molsys, box_shape='truncated octahedral', clearance='14.0 angstroms')

Wrap water molecules to the primary unit cell using the minimum image convention:

molsys = msm.pbc.wrap_to_mic(molsys)

Finally, visualize the solvated system:

msm.view(molsys)