Difference between revisions of "Test Set Construction SB2024 V1 DOCK6.10 A"
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==II.Scripts for System Preparation== | ==II.Scripts for System Preparation== | ||
Each script should process the system in a fully automated manner. There are key elements to check at each step before proceeding to the next. The output to be checked from each step is written to a folder "zzz.outfiles" with a unique file for each system, at each step. At the top of this file is the netid of the user who ran each process. | Each script should process the system in a fully automated manner. There are key elements to check at each step before proceeding to the next. The output to be checked from each step is written to a folder "zzz.outfiles" with a unique file for each system, at each step. At the top of this file is the netid of the user who ran each process. | ||
| − | ==A. Ligand Preparation== | + | ==A. Preliminary File Preparation== |
| + | The receptor and ligand should be prepared from the initial PDB file as outlined in student provided VS tutorials . Briefly | ||
| + | (1) The ligand should have hydrogens added with careful attention to protonation state and gasteiger charges added. The extracted ligand is saved as "${pdb_id}.lig.moe.mol2" . | ||
| + | (2) The receptor is saved in isolation. Generally any water molecules are deleted, except specialized experiments. Any atomic ions within 8 angstroms of the ligand are retained as part of the receptor. The protocols have prep and frcmod files integrated for Heme cofactors, so these should be retained as part of the receptor. Once the receptor, metal ions, and heme cofactor are extracted they are saved as "${pdb_id} | ||
| + | Any biologically relevant organic small molecule cofactor (such as NADH / NADPH) | ||
| + | ==B. Ligand Preparation== | ||
This step will assign am1bcc charges to the preliminary file $system.lig.moe.mol2 | This step will assign am1bcc charges to the preliminary file $system.lig.moe.mol2 | ||
| − | + | ==C. Receptor Preparation== | |
| − | == | + | ==D. Sphere Generation== |
| − | == | + | ==E. Single Grid Generation== |
| − | == | + | ==F. Multi Grid Generation== |
| − | == | + | ==G. Bookkeeping of Heavy Atoms== |
| − | == | ||
==III.Test Cases for Preparation Integrity== | ==III.Test Cases for Preparation Integrity== | ||
These are cases which that need to be visually inspected to ensure key operations during preparation were executed. This step is crucial after building the test set in batch mode. | These are cases which that need to be visually inspected to ensure key operations during preparation were executed. This step is crucial after building the test set in batch mode. | ||
Revision as of 17:55, 9 February 2024
!!!!!!Under Construction!!!!!!
The purpose of this tutorial is to develop a uniform method for adding systems to the Rizzo Lab test set, and rebuilding the set from initial files. This is the protocol to be used by all lab members. If the protocol is changed, a new tutorial should be made, preserving this tutorial.
Contents
- 1 I.Introduction
- 2 II.Scripts for System Preparation
- 3 A. Preliminary File Preparation
- 4 B. Ligand Preparation
- 5 C. Receptor Preparation
- 6 D. Sphere Generation
- 7 E. Single Grid Generation
- 8 F. Multi Grid Generation
- 9 G. Bookkeeping of Heavy Atoms
- 10 III.Test Cases for Preparation Integrity
- 11 IV.To Do
I.Introduction
A key development for this tutorial is bookkeeping scripts to manage the count of heavy atoms during processing and indicate unaccounted changes. Test cases are also included which should be visually inspected for indicated elements to be sure that processing occurred as expected.
II.Scripts for System Preparation
Each script should process the system in a fully automated manner. There are key elements to check at each step before proceeding to the next. The output to be checked from each step is written to a folder "zzz.outfiles" with a unique file for each system, at each step. At the top of this file is the netid of the user who ran each process.
A. Preliminary File Preparation
The receptor and ligand should be prepared from the initial PDB file as outlined in student provided VS tutorials . Briefly (1) The ligand should have hydrogens added with careful attention to protonation state and gasteiger charges added. The extracted ligand is saved as "${pdb_id}.lig.moe.mol2" . (2) The receptor is saved in isolation. Generally any water molecules are deleted, except specialized experiments. Any atomic ions within 8 angstroms of the ligand are retained as part of the receptor. The protocols have prep and frcmod files integrated for Heme cofactors, so these should be retained as part of the receptor. Once the receptor, metal ions, and heme cofactor are extracted they are saved as "${pdb_id} Any biologically relevant organic small molecule cofactor (such as NADH / NADPH)
B. Ligand Preparation
This step will assign am1bcc charges to the preliminary file $system.lig.moe.mol2
C. Receptor Preparation
D. Sphere Generation
E. Single Grid Generation
F. Multi Grid Generation
G. Bookkeeping of Heavy Atoms
III.Test Cases for Preparation Integrity
These are cases which that need to be visually inspected to ensure key operations during preparation were executed. This step is crucial after building the test set in batch mode.
| System | Element | Details |
|---|---|---|
| 2GQG | PhosphoTyrosine Residue | Check Residue 171 correctly has Y2P phosphotyrosine (See Picture below) |
| 2Y03 | Disulfide Bond | Check bond Residue 82.SG and Residue 167.SG is actually bonded (See Picture below ) |
| 4WMZ | Heme | Check Heme is correctly incorporated, including Iron (Fe) |
| 1P44 | NADH Cofactor | Make sure cofactor is present in 1P44.rec.clean.mol2 and grid.out as residue "COF" |
| 5UPG | Zinc Chelated Histidine Protonation | Residue should have HID protonation (See Picture below) |
| 3D94 | NonStandard Residue Defined Mutatation | Make sure Residue 146 successfully mutates to Residue "MET" from "MHO" |
IV.To Do
1. Integrate prep and frcmod files for cofactors available at http://amber.manchester.ac.uk/
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Tutorial Written By: Christopher Corbo, Rizzo Lab, Stony Brook University (2024)
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