Setting up modeling proteins

Prepare Applications

Before running QCLObot-modeler, AmberTools is required. Please set the environment variable, AMBERHOME.

Prepare Oxytocin model

You can get Oxytocin model (2MGO.pdb) from PDB or here.

The file (2,875 lines) begins as follows; download the full file via the link above.

HEADER    HORMONE                                 01-NOV-13   2MGO              
TITLE     NMR SOLUTION STRUCTURE OF OXYTOCIN                                    
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: OXYTOCIN;                                                  
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.               
KEYWDS    HORMONE                                                               
EXPDTA    SOLUTION NMR                                                          
NUMMDL    20                                                                    
AUTHOR    P.J.HARVEY,D.J.CRAIK                                                  
REVDAT   1   22-OCT-14 2MGO    0                                                
JRNL        AUTH   J.KOEHBACH,M.O'BRIEN,M.MUTTENTHALER,M.MIAZZO,M.AKCAN,        
JRNL        AUTH 2 A.G.ELLIOTT,N.L.DALY,P.J.HARVEY,S.ARROWSMITH,S.GUNASEKERA,   
JRNL        AUTH 3 T.J.SMITH,S.WRAY,U.GORANSSON,P.E.DAWSON,D.J.CRAIK,           
JRNL        AUTH 4 M.FREISSMUTH,C.W.GRUBER                                      
JRNL        TITL   OXYTOCIC PLANT CYCLOTIDES AS TEMPLATES FOR PEPTIDE G         
JRNL        TITL 2 PROTEIN-COUPLED RECEPTOR LIGAND DESIGN.                      

Create input file for QCLObot-modeler

You save the following text as 2MGO_modeling.yaml.

tasks:
  - name: 2MGO
    protonate:
      src: 2mgo.pdb
  - name: 2MGO_opt
    opt:
      reference: 2MGO
  - name: 2MGO_optx
    neutralize:
      reference: 2MGO_opt
      dest: 2MGO_optx.pdb
  - name: 2MGO_optx_mdwatx
    md:
      reference: 2MGO_optx
      solvation:
        method: cap
        model: TIP3PBOX
      belly_mask:
        - water
        - ions
  - name: 2MGO_optx_mdwatx_optwatx
    opt:
      reference: 2MGO_optx_mdwatx
      belly_mask:
        - water
        - ions
      dest: 2MGO_optx_mdwatx.pdb
     

Run QCLObot-modeler

$ ${PDF_HOME}/bin/QCLObot-modeler.py 2MGO_modeling.yaml