Difference between revisions of "Minimize protein-covalent ligand complex with AMBER"

From DISI
Jump to: navigation, search
(Created page with " This is for ligands that modify a specific residue. (1) Make a directory: mkdir coval_min cd coval_min/ (2) Download pdb file from the web: wget https://files.rcsb....")
 
Line 97: Line 97:
 
Uses chimera to add hydrogens:  
 
Uses chimera to add hydrogens:  
  
 +
[[File:2018_12_coval1.png|thumb|center|500px|Use chimera to add hydrogens]]
  
  

Revision as of 09:58, 17 December 2018

This is for ligands that modify a specific residue.

(1) Make a directory:

mkdir coval_min
cd coval_min/


(2) Download pdb file from the web:

 wget https://files.rcsb.org/view/5YY1.pdb


(3) Manually create 3 files using your favorate text editor:

a covalent ligand, lig.pdb:

keep the sidechain of the mofifed cystien:

cat 94F_bkup.pdb 
ATOM     89  CA  CYS A  12      29.215  -1.013  17.747  1.00 23.10           C  
ATOM     92  CB  CYS A  12      30.264  -1.172  18.849  1.00 23.68           C  
ATOM     93  SG  CYS A  12      29.632  -1.020  20.503  1.00 25.01           S  
ATOM   1385  C31 94F A 203      16.511  -4.125  24.817  1.00 32.17           C  
ATOM   1386  C30 94F A 203      15.606  -4.260  23.787  1.00 32.36           C  
ATOM   1387  C32 94F A 203      17.840  -3.910  24.531  1.00 31.54           C  
ATOM   1388  C29 94F A 203      16.037  -4.183  22.484  1.00 32.47           C  
ATOM   1389  C19 94F A 203      21.614  -2.199  22.881  1.00 29.12           C  
ATOM   1390  C5  94F A 203      23.964  -5.464  22.540  1.00 29.57           C  
ATOM   1391  C18 94F A 203      22.453  -3.293  22.771  1.00 29.13           C  
ATOM   1392  C23 94F A 203      18.284  -3.829  23.223  1.00 31.43           C  
ATOM   1393  C22 94F A 203      19.692  -3.612  23.019  1.00 29.79           C  
ATOM   1394  C24 94F A 203      17.372  -3.972  22.203  1.00 32.05           C  
ATOM   1395  C3  94F A 203      21.900  -4.565  22.770  1.00 29.39           C  
ATOM   1396  C2  94F A 203      20.533  -4.693  22.895  1.00 29.45           C  
ATOM   1397  C20 94F A 203      20.247  -2.347  23.012  1.00 29.51           C  
ATOM   1398  C7  94F A 203      23.836  -3.189  22.644  1.00 28.94           C  
ATOM   1399  C14 94F A 203      29.536   0.583  20.690  1.00 25.47           C  
ATOM   1400  C13 94F A 203      28.376   1.143  21.474  1.00 26.40           C  
ATOM   1401  C12 94F A 203      27.093   0.850  20.795  1.00 26.10           C  
ATOM   1402  C9  94F A 203      23.979  -0.953  21.731  1.00 28.62           C  
ATOM   1403  C17 94F A 203      25.969  -2.149  22.595  1.00 29.17           C  
ATOM   1404  C10 94F A 203      25.024  -0.390  20.794  1.00 28.12           C  
ATOM   1405  C16 94F A 203      26.678  -0.809  22.586  1.00 28.22           C  
ATOM   1406  C25 94F A 203      17.826  -3.897  20.794  1.00 32.91           C  
ATOM   1407  N4  94F A 203      22.652  -5.665  22.653  1.00 29.29           N  
ATOM   1408  N6  94F A 203      24.595  -4.289  22.534  1.00 29.70           N  
ATOM   1409  N8  94F A 203      24.523  -1.948  22.642  1.00 29.33           N  
ATOM   1410  N11 94F A 203      26.238   0.005  21.476  1.00 27.18           N  
ATOM   1411  O15 94F A 203      26.847   1.362  19.713  1.00 25.34           O  
ATOM   1412  F1  94F A 203      19.995  -5.935  22.878  1.00 29.69           F  
ATOM   1413  F26 94F A 203      16.791  -3.770  19.931  1.00 34.77           F  
ATOM   1414  F27 94F A 203      18.674  -2.862  20.538  1.00 31.92           F  
ATOM   1415  F28 94F A 203      18.495  -5.026  20.445  1.00 33.49           F  
ATOM   1416 CL   94F A 203      19.224  -0.960  23.165  1.00 29.22          CL  

change and make the numbering and naming consistent:

cat 94F.pdb 
ATOM   1382  CA  LIG A 203      29.215  -1.013  17.747  1.00 23.10           C  
ATOM   1383  CB  LIG A 203      30.264  -1.172  18.849  1.00 23.68           C  
ATOM   1384  SG  LIG A 203      29.632  -1.020  20.503  1.00 25.01           S  
ATOM   1385  C31 LIG A 203      16.511  -4.125  24.817  1.00 32.17           C  
ATOM   1386  C30 LIG A 203      15.606  -4.260  23.787  1.00 32.36           C  
ATOM   1387  C32 LIG A 203      17.840  -3.910  24.531  1.00 31.54           C  
ATOM   1388  C29 LIG A 203      16.037  -4.183  22.484  1.00 32.47           C  
ATOM   1389  C19 LIG A 203      21.614  -2.199  22.881  1.00 29.12           C  
ATOM   1390  C5  LIG A 203      23.964  -5.464  22.540  1.00 29.57           C  
ATOM   1391  C18 LIG A 203      22.453  -3.293  22.771  1.00 29.13           C  
ATOM   1392  C23 LIG A 203      18.284  -3.829  23.223  1.00 31.43           C  
ATOM   1393  C22 LIG A 203      19.692  -3.612  23.019  1.00 29.79           C  
ATOM   1394  C24 LIG A 203      17.372  -3.972  22.203  1.00 32.05           C  
ATOM   1395  C3  LIG A 203      21.900  -4.565  22.770  1.00 29.39           C  
ATOM   1396  C2  LIG A 203      20.533  -4.693  22.895  1.00 29.45           C  
ATOM   1397  C20 LIG A 203      20.247  -2.347  23.012  1.00 29.51           C  
ATOM   1398  C7  LIG A 203      23.836  -3.189  22.644  1.00 28.94           C  
ATOM   1399  C14 LIG A 203      29.536   0.583  20.690  1.00 25.47           C  
ATOM   1400  C13 LIG A 203      28.376   1.143  21.474  1.00 26.40           C  
ATOM   1401  C12 LIG A 203      27.093   0.850  20.795  1.00 26.10           C  
ATOM   1402  C9  LIG A 203      23.979  -0.953  21.731  1.00 28.62           C  
ATOM   1403  C17 LIG A 203      25.969  -2.149  22.595  1.00 29.17           C  
ATOM   1404  C10 LIG A 203      25.024  -0.390  20.794  1.00 28.12           C  
ATOM   1405  C16 LIG A 203      26.678  -0.809  22.586  1.00 28.22           C  
ATOM   1406  C25 LIG A 203      17.826  -3.897  20.794  1.00 32.91           C  
ATOM   1407  N4  LIG A 203      22.652  -5.665  22.653  1.00 29.29           N  
ATOM   1408  N6  LIG A 203      24.595  -4.289  22.534  1.00 29.70           N  
ATOM   1409  N8  LIG A 203      24.523  -1.948  22.642  1.00 29.33           N  
ATOM   1410  N11 LIG A 203      26.238   0.005  21.476  1.00 27.18           N  
ATOM   1411  O15 LIG A 203      26.847   1.362  19.713  1.00 25.34           O  
ATOM   1412  F1  LIG A 203      19.995  -5.935  22.878  1.00 29.69           F  
ATOM   1413  F26 LIG A 203      16.791  -3.770  19.931  1.00 34.77           F  
ATOM   1414  F27 LIG A 203      18.674  -2.862  20.538  1.00 31.92           F  
ATOM   1415  F28 LIG A 203      18.495  -5.026  20.445  1.00 33.49           F  
ATOM   1416 CL   LIG A 203      19.224  -0.960  23.165  1.00 29.22          CL  

Uses chimera to add hydrogens:

Use chimera to add hydrogens


a co-factory (gdp), gdp.pdb:

and a receptor, rec.pdb:


Here is a modified cystiene residue (this is without a charge and without a hydrogen):

cat CYM.prep 
    0    0    2

CYSTEINE without h and without charge for covalent 
                                                                
 CYM  INT     0                                                 
 CORR OMIT DU   BEG                                             
   0.00000                                                      
   1  DUMM  DU    M    0  -1  -2     0.000     0.000     0.000   0.00000
   2  DUMM  DU    M    1   0  -1     1.449     0.000     0.000   0.00000
   3  DUMM  DU    M    2   1   0     1.522   111.100     0.000   0.00000
   4  N     N     M    3   2   1     1.335   116.600   180.000  -0.41570
   5  H     H     E    4   3   2     1.010   119.800     0.000   0.27190
   6  CA    CX    M    4   3   2     1.449   121.900   180.000   0.02130
   7  HA    H1    E    6   4   3     1.090   109.500   300.000   0.11240
   8  CB    2C    3    6   4   3     1.525   111.100    60.000  -0.12310
   9  HB2   H1    E    8   6   4     1.090   109.500   300.000   0.11120
  10  HB3   H1    E    8   6   4     1.090   109.500    60.000   0.11120
  11  SG    SH    E    8   6   4     1.810   116.000   180.000  -0.23580
  12  C     C     M    6   4   3     1.522   111.100   180.000   0.59730
  13  O     O     E   12   6   4     1.229   120.500     0.000  -0.56790

IMPROPER                                                        
 -M   CA   N    H                                               
 CA   +M   C    O                                               
                                                                
DONE                                                            
STOP