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OSPREY Tutorial

A comprehensive tutorial on installing, setting up, and running OSPREY, a powerful protein design software. Learn how to install OSPREY, set up compute nodes, input structures, and run energy calculations using MPI. Includes instructions for 32-bit and 64-bit systems.

charlesjames
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OSPREY Tutorial

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  1. OSPREYTutorial Ivelin Georgiev Donald Lab Duke University

  2. Installation Setup Running OSPREY

  3. Installation Java mpiJava MPICH2 32-bit 64-bit √ may require special instructions

  4. Setup Compute Nodes Input Structure Rotamer Library Energy Function

  5. Compute Nodes Select MPI nodes: linux1 linux2 linux3 linux4 linux5 mpdboot mpdboot -n 5 -f mpd.hosts Select job-specific nodes: linux1 linux1 linux1 linux2 linux3 linux3 mpirun java OSPREY mpirun -machinefile ./machines -np 5 java -Xmx1024M KStar mpi -c KStar.cfg

  6. Input Structure REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 GLU A 63 CD OE1 OE2 missing atoms KiNG model delete possible over-constraint possible under-constraint

  7. Input Structure adding hydrogens proteins general compounds recommended: MolProbity recommended: Accelrys DS Visualizer Check: protonation states missing protons

  8. Input Structure His residues HIP HIE HID

  9. Input Structure steric shell • close to design site • significant speedup

  10. Input Structure Other considerations: • protein, ligand, cofactor • ligand: natural AA, small molecule • water molecules • no chain ID’s • unique residue numbers • protein-peptide, protein-protein • connectivity (good input structures)

  11. Input Structure Check and double-check!!!

  12. Rotamer Library rotamers Richardsons’ Penultimate proteins general compounds # dihed # rot name TYR 2 4 N CA CB CG CA CB CG CD1 62 90 -177 80 -65 -85 -65 -30 TYR 2 5 N CA CB CG CA CB CG CD1 62 90 -177 80 -65 -85 -65 -30 -65 -45 FCL 2 4 N CA CB CG CA CB CG CD1 62 90 -177 80 -65 -85 -65 -30 1 2 one rotamer

  13. Energy Function parm96a.dat all_amino94X.in all_nuc94_and_gr.in • atom types • dihedral parameters • vdW parameters • amino acids • partial charges • connectivity • general compounds • partial charges • connectivity add params for new atom types antechamber typically no changes add params for new compounds antechamber can modify partial charges user control: distance-dependent dielectric, dielectric value, vdW radii scaling, solvation energy scaling, dihedral energies switch

  14. Running OSPREY GMEC-based Ensemble-based Residue entropy

  15. GMEC-based mpirun -machinefile ./machines -np 5 java -Xmx1024M KStar mpi -c KStar.cfg doDEE System.cfg DEE.cfg input structure rotamer library energy function mutation search parameters doDEE energy minimization (MinDEE, BD, BRDEE) DACS 1 MET GLY ASP ARG FCL 6 0 2 18 3 unMinE: -273.75 minE: -273.75 bestE: -273.75 2 MET GLY ASP MET FCL 6 0 2 6 3 unMinE: -271.96 minE: -271.96 bestE: -273.75 3 MET GLY ASP ARG FCL 6 0 2 18 3 unMinE: -271.78 minE: -271.78 bestE: -273.75 1 MET GLY SER ARG FCL 6 3 2 18 2 unMinE: -276.50 minE: -276.50 bestE: -276.50 2 MET GLY SER ARG FCL 6 3 1 18 2 unMinE: -276.42 minE: -276.42 bestE: -276.50

  16. GMEC-based java -Xmx1024M KStar -c KStar.cfg genStructDEE System.cfg GenStruct.cfg input structure rotamer library energy function struct generation parameters genStructDEE energy minimization (MinDEE, BD, BRDEE) 1 MET GLY SER ARG FCL 6 3 2 18 2 unMinE: -276.50 minE: -276.50 bestE: -276.50 2 MET GLY SER ARG FCL 6 3 1 18 2 unMinE: -276.42 minE: -276.42 bestE: -276.50 3 MET GLY ASP ARG FCL 6 0 2 18 3 unMinE: -273.75 minE: -273.75 bestE: -273.75 1 MET GLY ASP ARG FCL 6 0 2 18 3 unMinE: -273.75 minE: -273.75 bestE: -273.75 2 MET GLY ASP MET FCL 6 0 2 6 3 unMinE: -271.96 minE: -271.96 bestE: -273.75 3 MET GLY ASP ARG FCL 6 0 2 18 3 unMinE: -271.78 minE: -271.78 bestE: -273.75 1 MET GLY SER ARG FCL 6 3 2 18 2 unMinE: -276.50 minE: -276.50 bestE: -276.50 2 MET GLY SER ARG FCL 6 3 1 18 2 unMinE: -276.42 minE: -276.42 bestE: -276.50 rank

  17. Ensemble-based: Protein-ligand binding mpirun -machinefile ./machines -np 5 java -Xmx1024M KStar mpi KSMaster System.cfg MutSearch.cfg bound structure rotamer library energy function K* mutation search parameters KSMaster energy minimization (MinDEE, BD, BRDEE) doSinglePartFn 1 4.25E+24 ILE TRP ILE ALA ALA ILE 2 3.12E+24 TRP ASP ILE GLY ALA ILE 3 2.18E+24 ILE THR ILE PHE ALA ILE 4 1.45E+24 VAL THR ILE PHE ALA ILE 5 1.41E+24 ILE THR ILE TYR ALA ILE

  18. Residue entropy mpirun -machinefile ./machines -np 5 java -Xmx1024M KStar mpi doResEntropy System.cfg ResEntropy.cfg input structure rotamer library energy function mutation search parameters doResEntropy entropy res ID # prox res AA probabilities 257 2.33 0.2 0.0 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.1 0.0 0.0 0.0 0.2 0.0 0.1 18 481 2.29 0.2 0.0 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.0 0.0 0.0 0.1 0.0 0.1 15 32 2.29 0.3 0.0 0.1 0.1 0.0 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.0 0.1 23 26 2.28 0.2 0.0 0.1 0.0 0.0 0.1 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.2 0.0 0.0 0.1 0.1 0.0 29 163 2.26 0.3 0.0 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.0 0.0 0.0 0.1 0.0 0.1 0.0 0.1 22

  19. Some important parameters mpirun -machinefile ./machines -np 5 java -Xmx1024M KStar mpi -c KStar.cfg doDEE System.cfg DEE.cfg KStar.cfg: hElect true hVDW false hSteric false distDepDielect true dielectConst 6.0 vdwMult 0.95 doDihedE true doSolvationE true solvScale 0.8 stericThresh 0.4 softStericThresh 1.5 rotFile LovellRotamer.dat grotFile GenericRotamers.dat volFile AAVolumes.dat energy function steric filter rotamer libraries volume filter

  20. Some important parameters mpirun -machinefile ./machines -np 5 java -Xmx1024M KStar mpi -c KStar.cfg doDEE System.cfg DEE.cfg System.cfg: pdbName 1amuFH.pdb numInAS 4 residueMap 239 278 299 301 pdbLigNum 566 ligAA false numCofRes 1 cofMap 567 input pdb design site ligand cofactor

  21. Some important parameters mpirun -machinefile ./machines -np 5 java -Xmx1024M KStar mpi -c KStar.cfg doDEE System.cfg DEE.cfg DEE.cfg (partial): doDACS true distrDACS false initDepth 2 subDepth 1 diffFact 6 doMinimize false minimizeBB false doBackrubs false backrubFile none useEref true ligPresent false ligType none resAllowed0 gly ala val leu ile tyr phe trp met … resAllowed3 gly ala val leu ile tyr phe trp met resumeSearch false resumeFilename runInfo.out.partial DACS minimization reference energies ligand in search allowed mutations resuming

  22. Some important parameters mpirun -machinefile ./machines -np 5 java -Xmx1024M KStar mpi KSMaster System.cfg MutSearch.cfg MutSearch.cfg (partial): mutFileName 1amuFCL_2MUT.mut numMutations 2 targetVolume 620.0 volumeWindow 100000000.0 doMinimize false minimizeBB false doBackrubs false backrubFile none epsilon 0.03 gamma 0.01 repeatSearch true useUnboundStruct false unboundPdbName none resAllowed0 gly ala val leu ile tyr phe trp met resumeSearch false resumeFilename 1amuFCL_MutSearch.partial volume filter/ candidate mutants minimization (1-ε) accuracy inter-mutation at most 1 repeat unbound struct allowed mutations resuming

  23. General citation: Citing OSPREY K* and MinDEE: BD: BRDEE: DACS: Original K* publication:

  24. OSPREY is open source!!!

  25. Acknowledgements Bruce Donald Ryan Lilien Faisal Reza Kyle Roberts Daniel Keedy Pablo Gainza Donald Lab Funding: • NIH

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