Make cg_openmm pdbs consistent with cg_pyrosetta pdbs?

mrshirts commented 4 years ago

If we want to be running the same analysis codes, we should probably make the pdbs consistent. @tlfobe, can you post an example foldamer pdb file that you generated with cg_pyrosetta?

mrshirts commented 4 years ago

So, for Pyrosetta, the residue file looks like this:

# rosetta residue topology file
# custom atom residue
# Author : Lenny Fobe
NAME CG11x3
IO_STRING CG11x3 X
TYPE POLYMER
AA UNK
ATOM BB1 CG1 CG1 0  # 1 bead backbone
ATOM BB2 CG1 CG1 0  # 
ATOM BB3 CG1 CG1 0  # 
ATOM SC1 CG2 CG2 0  # 1 bead sidechain
ATOM SC2 CG2 CG2 0  # repeated 2x
ATOM SC3 CG2 CG2 0  # 
LOWER_CONNECT BB1
UPPER_CONNECT BB3
BOND BB1 SC1
BOND BB1 BB2
BOND BB2 SC2
BOND BB2 BB3
BOND BB3 SC3
FIRST_SIDECHAIN_ATOM SC1
PROPERTIES ACHIRAL_BACKBONE
NBR_ATOM SC1
NBR_RADIUS 7.5
ICOOR_INTERNAL    BB1    0.000000    0.000000    0.000000    BB1    BB2   BB3
ICOOR_INTERNAL    BB2    0.000000  180.000000    1.000000    BB1    BB2   BB3
ICOOR_INTERNAL    BB3    0.000000   60.000000    1.000000    BB2    BB1   BB3
ICOOR_INTERNAL    SC1    0.000000   60.000000    1.000000    BB1    BB2   BB3
ICOOR_INTERNAL    SC2    0.000000  -60.000000    1.000000    BB2    BB1   SC1
ICOOR_INTERNAL    SC3    0.000000  -60.000000    1.000000    BB3    BB2   BB1
ICOOR_INTERNAL   UPPER   0.000000   60.000000    1.000000    BB3    BB2   BB1
ICOOR_INTERNAL   LOWER   0.000000  -60.000000    1.000000    BB1    BB2   BB3

mrshirts commented 4 years ago

And the PDB looks like this:

HEADER                                            20-JUL-20   XXXX              
EXPDTA    THEORETICAL MODEL                                                     
REMARK 220                                                                      
REMARK 220 EXPERIMENTAL DETAILS                                                 
REMARK 220  EXPERIMENT TYPE                : THEORETICAL MODELLING              
REMARK 220  DATE OF DATA COLLECTION        : 20-JUL-20                          
REMARK 220                                                                      
REMARK 220 REMARK: MODEL GENERATED BY ROSETTA                                   
REMARK 220  VERSION 2020.25.post.dev+102.tlfobe.addatomsflag.b71eaaec7          
HETATM    1 BB1  CG1 A   1       0.000  -0.000  -0.000  1.00  0.00           X  
HETATM    2 BB2  CG1 A   1       1.000   0.000   0.000  1.00  0.00           X  
HETATM    3 BB3  CG1 A   1       1.572   0.019   0.820  1.00  0.00           X  
HETATM    4 SC1  CG1 A   1      -0.462   0.368   0.807  1.00  0.00           X  
HETATM    5 SC2  CG1 A   1       1.461   0.070  -0.885  1.00  0.00           X  
HETATM    6 SC3  CG1 A   1       2.422   0.545   0.773  1.00  0.00           X  
HETATM    7 BB1  CG1 A   2       1.299  -0.331   1.715  1.00  0.00           X  
HETATM    8 BB2  CG1 A   2       0.506  -0.916   1.884  1.00  0.00           X  
HETATM    9 BB3  CG1 A   2       0.014  -1.432   1.183  1.00  0.00           X  
HETATM   10 SC1  CG1 A   2       1.881  -0.106   2.497  1.00  0.00           X  
HETATM   11 SC2  CG1 A   2       0.155  -0.960   2.820  1.00  0.00           X  
HETATM   12 SC3  CG1 A   2      -0.984  -1.374   1.182  1.00  0.00           X  
HETATM   13 BB1  CG1 A   3       0.440  -2.046   0.518  1.00  0.00           X  
HETATM   14 BB2  CG1 A   3       1.199  -1.796  -0.083  1.00  0.00           X  
HETATM   15 BB3  CG1 A   3       2.145  -1.663   0.213  1.00  0.00           X  
HETATM   16 SC1  CG1 A   3      -0.019  -2.916   0.338  1.00  0.00           X  
HETATM   17 SC2  CG1 A   3       1.017  -1.767  -1.066  1.00  0.00           X  
HETATM   18 SC3  CG1 A   3       2.847  -1.601  -0.496  1.00  0.00           X  
HETATM   19 BB1  CG1 A   4       2.443  -1.594   1.165  1.00  0.00           X  
HETATM   20 BB2  CG1 A   4       2.080  -2.140   1.920  1.00  0.00           X  
HETATM   21 BB3  CG1 A   4       1.365  -2.834   1.832  1.00  0.00           X  
HETATM   22 SC1  CG1 A   4       3.235  -1.014   1.358  1.00  0.00           X  
HETATM   23 SC2  CG1 A   4       2.426  -1.948   2.838  1.00  0.00           X  
HETATM   24 SC3  CG1 A   4       0.613  -2.807   2.490  1.00  0.00           X  
HETATM   25 BB1  CG1 A   5       1.390  -3.601   1.191  1.00  0.00           X  
HETATM   26 BB2  CG1 A   5       1.922  -3.624   0.345  1.00  0.00           X  
HETATM   27 BB3  CG1 A   5       1.555  -3.842  -0.559  1.00  0.00           X  
HETATM   28 SC1  CG1 A   5       0.890  -4.430   1.444  1.00  0.00           X  
HETATM   29 SC2  CG1 A   5       2.897  -3.407   0.407  1.00  0.00           X  
HETATM   30 SC3  CG1 A   5       1.966  -3.385  -1.347  1.00  0.00           X  
TER                                                                             
CONECT    1    2    4                                                           
CONECT    2    1    3    5                                                      
CONECT    3    2    6    7                                                      
CONECT    4    1                                                                
CONECT    5    2                                                                
CONECT    6    3                                                                
CONECT    7    3    8   10                                                      
CONECT    8    7    9   11                                                      
CONECT    9    8   12   13                                                      
CONECT   10    7                                                                
CONECT   11    8                                                                
CONECT   12    9                                                                
CONECT   13    9   14   16                                                      
CONECT   14   13   15   17                                                      
CONECT   15   14   18   19                                                      
CONECT   16   13                                                                
CONECT   17   14                                                                
CONECT   18   15                                                                
CONECT   19   15   20   22                                                      
CONECT   20   19   21   23                                                      
CONECT   21   20   24   25                                                      
CONECT   22   19                                                                
CONECT   23   20                                                                
CONECT   24   21                                                                
CONECT   25   21   26   28                                                      
CONECT   26   25   27   29                                                      
CONECT   27   26   30                                                           
CONECT   28   25                                                                
CONECT   29   26                                                                
CONECT   30   27                                                                
# All scores below are weighted scores, not raw scores.
#BEGIN_POSE_ENERGIES_TABLE /home/lenny/Research/cg_pyrosetta/examples/parameter_scan/signac/workspace/320af501f7c7ec18059bcd6842666ff5/minimum.pdb
label fa_atr fa_rep fa_intra_atr fa_intra_rep mm_twist mm_bend total
weights 1 1 1 1 1 1 NA
pose -20.0592 1.11747 -0.66326 0.00647 0 0.22577 -19.3728
CG11x3:CGLower_1 -3.66453 0.24529 -0.15083 0.00025 0 0.05231 -3.5175
CG11x3_2 -3.86864 0.17887 -0.12547 0.00097 0 0.05329 -3.76099
CG11x3_3 -5.24752 0.31865 -0.13013 0.00276 0 0.08562 -4.97062
CG11x3_4 -4.20802 0.24766 -0.12591 0.00242 0 0.0272 -4.05665
CG11x3:CGUpper_5 -3.07051 0.127 -0.13092 7e-05 0 0.00734 -3.06702
#END_POSE_ENERGIES_TABLE /home/lenny/Research/cg_pyrosetta/examples/parameter_scan/signac/workspace/320af501f7c7ec18059bcd6842666ff5/minimum.pdb

mrshirts commented 4 years ago

Makes me think:

Maybe we should use HETATM instead of ATOM in CG OpenMM, since these aren't true atoms.
We might want to add more HEADER and REMARK entries to the CG openmm output, but they do not need to be the same between cg_openmm and cg_pyrosetta.
We want to screen out the #BEGIN_POSE_ENERGIES_TABLE / #END_POSE_ENERGIES_TABLE from pyrosetta pdb analysis.
Otherwise, it mostly seems to just be naming conventions of the residues and atoms.

mrshirts commented 4 years ago

@tlfobe, how come the CG2 entry in the residue data doesn't end up in the pdb? Or are CG1 and CG2 particle name types that shouldn't show up in the pdb, and the residue name is just CG11x3 truncated to the first three characters (i.e. CG1)?

shirtsgroup / analyze_foldamers

Make cg_openmm pdbs consistent with cg_pyrosetta pdbs? #5