Generate index files for gmx angle command

User discussions
,
1

GROMACS version: 2022.2
GROMACS modification: No
Here post your question

Hi All,

I need to create an index file containing angles using the “gmx mk_angndx” command.

“gmx mk_angndx -s prd.tpr -n angle.ndx -type angle -hq -1” This was the command I used for that. But this gave me an empty output file.

My system contains water molecules. Does anyone know the reason for the empty output file?

Thank you
Kalpani

2

From what I understand, I don’t think mk_angndx returns indices for water molecules (at least I couldn’t find a way to get it to do so, if someone knows how then please correct me), if you were to simulate a protein in your system, then the command should work for the atoms of that protein.

You should be able to find the data on the angles of the water molecules from the .itp file of the water model you used in the folder containing your forcefield.

3

Thank you very much.