Hello,
I am trying calculate non bonded interactions between aminoacid resides derived from ligand and protein pocket. Firstly I prepare index file in the following way:
gmx make_ndx -f complex.pdb -o index
where complex.pdb is a pdb file, which contains all cartesian coordinates for all atoms from ligand and protein
Then, I used to calculation non bonded energy the following command:
gmx energy -f complex.pdb -o nonbonded_interactions.xvg -n index.ndx
And after this command I get the following error:
Function: void gmx::CommandLineParser::parse(int*, char**)
Error in user input:
Invalid command-line options
In command-line option -f
File name ‘complex.pdb’ cannot be used for this option.
Only the following extensions are possible:
.edr
Unknown command-line option -n
I am totally beginner user in gromacs software. Could you please help me to solve this error or indicate another way or command to calculate these interactions ?
Best regards