prepare a gromacs index.ndx file which contains two groups named RECEPTOR and LIGAND

[CNDOTA]

Dear authors,

Very nice tool!

I want to ask for some help.

After running the unigbsa-md command, I got the "1ceb_ligand.mol", "complex.gro", "complex.pdb", "complex.top", and "traj_comx.xtc" files.

And I want to run the unigbsa-traj command, however, it needs to prepare a gromacs index.ndx file which contains two groups named RECEPTOR and LIGAND. Although I refer to https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html, it is still not clear.

Could you specify the command of how to prepare this file?

Thank you very much!

[Aunity]

Here is an example for generating an index.ndx file. Firstly, we need the complex.pdb or complex.gro file and run this command:

gmx make_ndx -f complex.pdb
# or 
gmx make_ndx -f complex.gro

And you will see this in your screen:

             :-) GROMACS - gmx make_ndx, 2020.1-Ubuntu-2020.1-1 (-:

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GROMACS:      gmx make_ndx, version 2020.1-Ubuntu-2020.1-1
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /root/ymh/Uni-GBSA/example/scan/test/1a
Command line:
  gmx make_ndx -f complex.pdb

Reading structure file
Going to read 0 old index file(s)
Analysing residue names:
There are:     1      Other residues
There are:   212    Protein residues
There are:     1        Ion residues
There are:   260      Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
Analysing Protein...
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...

  0 System              :  4104 atoms
  1 Other               :    27 atoms
  2 MOL                 :    27 atoms
  3 ZN                  :     1 atoms
  4 Protein             :  3296 atoms
  5 Protein-H           :  1679 atoms
  6 C-alpha             :   208 atoms
  7 Backbone            :   628 atoms
  8 MainChain           :   838 atoms
  9 MainChain+Cb        :  1025 atoms
 10 MainChain+H         :  1040 atoms
 11 SideChain           :  2256 atoms
 12 SideChain-H         :   841 atoms
 13 Prot-Masses         :  3296 atoms
 14 non-Protein         :   808 atoms
 15 Ion                 :     1 atoms
 16 MOL                 :    27 atoms
 17 ZN                  :     1 atoms
 18 Water               :   780 atoms
 19 SOL                 :   780 atoms
 20 non-Water           :  3324 atoms
 21 Water_and_ions      :   781 atoms

 nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
 'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
 't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
 'r': residue              'res' nr         'chain' char
 "name": group             'case': case sensitive           'q': save and quit
 'ri': residue index

>

Since group 4 represents the RECEPTOR group, we assign the name RECEPTOR to group 4 by entering the command name 4 RECEPTOR and then pressing Enter.

Similarly, group 2 represents the LIGAND group. We assign the name LIGAND to group 2 by using the command name 2 LIGAND and then pressing Enter.

Once you have named both groups, type q to quit. This will generate an index file that includes both RECEPTOR and LIGAND.

[CNDOTA]

Thank you very much!