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Amber: How to Prepare Parameters for Non-standard Residues.

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Presentation on theme: "Amber: How to Prepare Parameters for Non-standard Residues."— Presentation transcript:

1 Amber: How to Prepare Parameters for Non-standard Residues

2 Requirements 1.Amber Modules: xleap/tleap, antechamber, parmchk, Gaussian (not a part of Amber) 2.Molecule Editor 3.Text Editor

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

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

5 Parameter Derivation

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

7 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

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

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

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

11 Appendix

12 Inhibitor covalently bonded to the Ser-195 of a protein

13 SEP (Ser-195) PPH


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