GROMACS version:2022
GROMACS modification: No
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I am unable to create an index file for carbonyl carbon of the peptide bond in protein for rmsd calculation?
I tried using
echo -e “r CO\na C & same residue as (name CA)\nq” | gmx make_ndx -f em.tpr -o index_carbonyl.ndx
But it is giving errors like
Found 0 atoms with residue name CO
Group is empty
Found 40 atoms with name C
Syntax error: “same residue as (name CA)”
I have also tried various other ways but it seems the syntax cannnot recognize & | and same residue.
Could someone help