[gmx-users] setting distance restraints between atoms belonging to different residues (Alessandra Villa)

[Sadaf Rani]

Hi Alessandra
I used it but top file extension is not supported. Should I give a combined
PDB file? I got ligand topology from an external server when I will give
combined PDB, it will give an error for not having these residues in the
database.

Could you please suggest which file should I give?

Here is undermentioned command which I used for the -merge option.

gmx pdb2gmx -f G6PD_topol.top -merge G6P_topol.top


-------------------------------------------------------
Program:     gmx pdb2gmx, version 2019.4
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 276)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -f
    File name 'G6PD_topol.top' cannot be used for this option.
    Only the following extensions are possible:
      .gro, .g96, .pdb, .brk, .ent, .esp, .tpr
  In command-line option -merge
    Invalid value: G6P_topol.top

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


Thanks

Sadaf