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I have been trying to get the CG representation of a basic octane molecule. The pdb file is as follows:

ATOM      1  C1  BUT     1       2.142   1.395  -8.932  1.00  0.00
ATOM      2  C2  BUT     1       3.631   1.416  -8.537  1.00  0.00
ATOM      3  C3  BUT     1       4.203  -0.012  -8.612  1.00  0.00
ATOM      4  C4  BUT     1       5.691   0.009  -8.218  1.00  0.00
ATOM      5 1H1  BUT     1       1.604   0.760  -8.260  1.00  0.00
ATOM      6 2H1  BUT     1       1.745   2.388  -8.880  1.00  0.00
ATOM      7 3H1  BUT     1       2.043   1.024  -9.930  1.00  0.00
ATOM      8 1H2  BUT     1       4.169   2.051  -9.210  1.00  0.00
ATOM      9 2H2  BUT     1       3.731   1.788  -7.539  1.00  0.00
ATOM     10 1H3  BUT     1       3.665  -0.647  -7.940  1.00  0.00
ATOM     11 2H3  BUT     1       4.104  -0.384  -9.610  1.00  0.00
ATOM     12 1H4  BUT     1       5.793   0.388  -7.201  1.00  0.00
ATOM     13 2H4  BUT     1       6.240   0.656  -8.903  1.00  0.00
ATOM     14  C1  MET     1       6.263  -1.418  -8.293  1.00  0.00
ATOM     15 1H1  MET     1       6.162  -1.797  -9.309  1.00  0.00
ATOM     16 2H1  MET     1       5.715  -2.065  -7.608  1.00  0.00
ATOM     17  C1  MET     1       7.750  -1.397  -7.899  1.00  0.00
ATOM     18 1H1  MET     1       7.852  -1.018  -6.882  1.00  0.00
ATOM     19 2H1  MET     1       8.299  -0.750  -8.583  1.00  0.00
ATOM     20  C1  MET     1       8.321  -2.824  -7.973  1.00  0.00
ATOM     21 1H1  MET     1       8.221  -3.203  -8.990  1.00  0.00
ATOM     22 2H1  MET     1       7.774  -3.471  -7.288  1.00  0.00
ATOM     23  C1  MET     1       9.809  -2.803  -7.579  1.00  0.00
ATOM     24 1H1  MET     1      10.214  -3.813  -7.632  1.00  0.00
ATOM     25 2H1  MET     1      10.358  -2.156  -8.264  1.00  0.00
ATOM     26 3H1  MET     1       9.911  -2.424  -6.562  1.00  0.00
TER      27      MET     1 
END

I cannot understand how to run martinize.py once I have downloaded the whole repo from the source: https://github.com/cgmartini/martinize.py/tree/master . Do I run it as a shell script, if yes what is the command I should use to run MARTINI to merely get the CG .pdb representation of an AA .pdb

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As per the README we can invoke martinize as follows:

martinize.py -i input.pdb -o output.pdb

I ran the command on a PDB of 4poj

And I get the following output files:

output.pdb

#include "martini.itp"
#include "Protein_A.itp"
#include "Protein_B.itp"

[ system ]
; name
Martini system from /content/drive/MyDrive/input_files/PDB/4poj.pdb

[ molecules ]
; name        number
Protein_A    1
Protein_B    1

Protein_A.itp (pasting only a subset of the full file here since the file exceeds line limit in MMSE)

; MARTINI (martini22) Coarse Grained topology file for "Protein_A"
; Created by martinize.py version 2.6 
; Using the following options:  -f /content/drive/MyDrive/input_files/PDB/4poj.pdb -o output.pdb
; Sequence:
; EDMPVERILEAELAVEPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP
; Secondary Structure:
; CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC

[ moleculetype ]
; Name         Exclusions
Protein_A         1

[ atoms ]
    1    Qd     1   GLU    BB     1  1.0000 ; C
    2    Qa     1   GLU   SC1     2 -1.0000 ; C
    3    P5     2   ASP    BB     3  0.0000 ; C
    4    Qa     2   ASP   SC1     4 -1.0000 ; C
    5    P5     3   MET    BB     5  0.0000 ; C
    6    C5     3   MET   SC1     6  0.0000 ; C
    7    P4     4   PRO    BB     7  0.0000 ; C
    8    C3     4   PRO   SC1     8  0.0000 ; C
    9    P5     5   VAL    BB     9  0.0000 ; C
   10   AC2     5   VAL   SC1    10  0.0000 ; C
   11    P5     6   GLU    BB    11  0.0000 ; C
   12    Qa     6   GLU   SC1    12 -1.0000 ; C
   13    P5     7   ARG    BB    13  0.0000 ; C
   14    N0     7   ARG   SC1    14  0.0000 ; C
   15    Qd     7   ARG   SC2    15  1.0000 ; C
   16    P5     8   ILE    BB    16  0.0000 ; C
   17   AC1     8   ILE   SC1    17  0.0000 ; C
   18    P5     9   LEU    BB    18  0.0000 ; C
   19   AC1     9   LEU   SC1    19  0.0000 ; C
   20    P5    10   GLU    BB    20  0.0000 ; C
   21    Qa    10   GLU   SC1    21 -1.0000 ; C
   22    P4    11   ALA    BB    22  0.0000 ; C
   23    P5    12   GLU    BB    23  0.0000 ; C
   24    Qa    12   GLU   SC1    24 -1.0000 ; C
   25    P5    13   LEU    BB    25  0.0000 ; C

Protein_B.itp

; MARTINI (martini22) Coarse Grained topology file for "Protein_B"
; Created by martinize.py version 2.6 
; Using the following options:  -f /content/drive/MyDrive/input_files/PDB/4poj.pdb -o output.pdb
; Sequence:
; KHKILHRLLQD
; Secondary Structure:
; CCCCCCCCCCC

[ moleculetype ]
; Name         Exclusions
Protein_B         1

[ atoms ]
    1    Qd     1   LYS    BB     1  1.0000 ; C
    2    C3     1   LYS   SC1     2  0.0000 ; C
    3    Qd     1   LYS   SC2     3  1.0000 ; C
    4    P5     2   HIS    BB     4  0.0000 ; C
    5   SC4     2   HIS   SC1     5  0.0000 ; C
    6   SP1     2   HIS   SC2     6  0.0000 ; C
    7   SP1     2   HIS   SC3     7  0.0000 ; C
    8    P5     3   LYS    BB     8  0.0000 ; C
    9    C3     3   LYS   SC1     9  0.0000 ; C
   10    Qd     3   LYS   SC2    10  1.0000 ; C
   11    P5     4   ILE    BB    11  0.0000 ; C
   12   AC1     4   ILE   SC1    12  0.0000 ; C
   13    P5     5   LEU    BB    13  0.0000 ; C
   14   AC1     5   LEU   SC1    14  0.0000 ; C

When I ran the command on your PDB file, the code seems to throw an error. Without the -o option on your file, this is what the code outputs for your PDB file:

INFO       MARTINIZE, script version 2.6
INFO       If you use this script please cite:
INFO       de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO       Chain termini will be charged
INFO       Residues at chain brakes will not be charged
INFO       The martini22 forcefield will be used.
INFO       Local elastic bonds will be used for extended regions.
INFO       Read input structure from file.
INFO       Input structure is a PDB file.
INFO       Found 2 chains:
INFO          1:    (Unknown), 13 atoms in 1 residues.
INFO          2:    (Protein), 13 atoms in 1 residues.
INFO       Removing HETATM chain  consisting of 1 residues.
INFO       Total size of the system: 1 residues.
WARNING    No secondary structure or determination method speficied. Protein chains will be set to 'COIL'.
INFO       Note: Cysteine bonds are 0.24 nm constraints, instead of the published 0.39nm/5000kJ/mol.

    There you are. One MARTINI. Shaken, not stirred.


And when that first martini hits the liver like a silver bullet, there is a sigh of contentment that can be heard in Dubuque. 
                                                          --William Emerson, Jr.
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  • $\begingroup$ How do I get from a .gro file to a .pdb file? $\endgroup$
    – Pranoy Ray
    Commented Jan 31 at 16:02
  • $\begingroup$ GROMACS provides a tool called editconf that can be used to convert GRO files to PDB format. Use the following command: gmx editconf -f input.gro -o output.pdb $\endgroup$
    – Vandan Revanur
    Commented Feb 4 at 19:00

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