Modified Amino Acids

Phosphorylated amino acid parameters

There are phosphorylated amino acid parameters for each of the force fields listed below. Choose the set that matches.

ff99SB

Parameters for phosphorylated amino acids compatible with ff99SB and older forcefields can be obtained with the following command in LEaP:

source leaprc.phosaa10

Updated parameters for the new versions of the Stony Brook (SB) family of forcefields include new parameters for the side chains of phosphorylated amino acids and common modified amino acids such as FRET and EPR. The modified amino acids selenomethionine, cyano-phenylalanine, and azido-phenylalanine are used as FRET quenchers. Parameters for acetylated lysine and nitoxide spin-label methanesulfonothioate (MTSL) which are used to probe distances in EPR experiments were also added. These side-chain parameters are optimized for use with ff14SB and ff19SB.

ff14SB

For ff19SB, parameters for phosphoylated amino acids can be obtained with the following command in LEaP:

source leaprc.phosaa14SB

Modified amino acid parameters can be obtained using the following commanp in LEaP:

source leaprc.protein.ff14SB_modAA

This conmmand will load lib and frcmod files that have the CX to XC atom type conversion, the backbone ph/psi dihedrals will be zeroed, and the LEI CMAP will be applied to all five residues. The residue names for these modified amino acids are MSE (selelnomethionine), AZF (azido-phenylalanine), CYF (cyano=phenylalanine), CNX(MTTSL) and ALY (acetylated-lysine). These residue names should match those in the loaded file with the coordinates (ex. PDB). The residue names can also be used with the sequence command in LEaP to create XYZ coordinates.

ff19SB

For ff19SB, parameters for phsphorylated amino acids can be obtained with the following command in LEaP:

source leaprc.phosaa19SB

Modified amino acid parameters can be obtained using the following commanp in LEaP:

source leaprc.protein.ff14SB_modAA

Un-natural amino acids

The expanded ff15ipq protein force field (ff15ipq-m) enable the modeling of artificial backbone units that are commonly used alongside natural ɑ residues in blended backbones of protein memetics. This includes chirality-reversed D-ɑ-residues, C_ɑ -methylated ɑ-residue Aib, homologated β- residues bearing proteinogenic side chains, and two cyclic β residues: APC and ACPC.

An expanded version of of the ff15ipq protein force field, denoted as ff15ipq-m, can be obtained with the following command.

source leaprc.mimetic.ff15ipq

Parameters for fluorinated, aromatic amino acids to be used with the ff15ipq protein forcefield can be obtained with the following command.

source leaprc.fluorine.ff15ipq

For a tutorial on using this forcefield please see this tutorial.

For more information on modified amino acids, please check out the Amber Reference Manual.