Amber: How to Prepare Parameters for Non-standard Residues

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Presentation transcript:

Amber: How to Prepare Parameters for Non-standard Residues

Requirements Amber Modules: xleap/tleap, antechamber, parmchk, Gaussian (not a part of Amber) Molecule Editor Text Editor

Parameter Preparation Workflow Using Gaussian Structure Output with ESP Info Text Editor Gaussian antechamber Residue Structure parmchk prepin file frcmod file Molecule Editor Xleap/tleap Lib File

Molecular/Structure Editors Freeware (not many) Xleap (very basic editor facilities) Sirius sirius.sdsc.edu/ JMolEditor sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html Commercial Software Sybyl, HyperChem, Spartan, GaussView, etc.

Parameter Derivation

Parameter Derivation: Partial Charges QM = ab initio, DFT, semi-empirical

Parameter Derivation: Van der Waals Parameters It is the most difficult part… 1) Optimizing van der Waals parameters to reproduce the experimental or high-level Quantum Chemical data Could be computationally expensive 2) Optimizing van der Waals parameters through the Monte Carlo or MD simulations to reproduce the experimental properties of bulk solvent (density, etc.). For example, OPLS van der Waals parameters Could be computationally expensive 3) Reusing existing van der Waals parameters for similar atom types from the same or other force field The simplest approach

Parameter Derivation: Bond and Angle Interactions req and θeq come either from experimental data (X-ray, neutron diffraction) or Quantum Chemical calculations (geometry optimization) Kr and Kθ force constants are usually optimized to reproduce the vibration frequencies calculated using high-level Quantum Chemical methods. Or (the simplest approach) Kr and Kθ force constants could be derived from the existing bond/angle parameters for similar bond/angle types from the same or other force field

Parameter Derivation: Dihedral Angle Interactions Vn, n, and γ are derived to reproduce the rotational profile from the high-level Quantum Chemical calculations. Or (the simplest approach) Vn, n, and γ could be derived from the existing dihedral angle parameters for similar dihedral angle types from the same or other force field J.Wang et al., Development and testing of a general amber force field, Journal of Computational Chemistry, 25 (2004), 1157

Parameter Preparation Workflow Using Gaussian Output with ESP Info Derived Parameters antechamber parmchk prepin file frcmod file Parameter modification file Xleap/tleap Lib File Description of residue(s)

Appendix

Inhibitor covalently bonded to the Ser-195 of a protein

SEP (Ser-195) PPH