Hi,

I am trying to calculate the conformational entropy for the heavy atoms of a protein but GROMACS-2016.4 doesn’t give a number.

Here are my commands:

echo ‘C-alpha Protein-H\n’ | gmx covar -s complex.tpr -f complex.xtc

echo | gmx anaeig -v eigenvec.trr -entropy

```
The Entropy due to the Quasi Harmonic approximation is inf J/mol K
The Entropy due to the Schlitter formula is -nan J/mol K
```

However, it gives a number for both Quasi Harmonic approximation and Schlitter formula when I select the C-alpha atoms. Could you please tell me how I can calculate the conformational entropy for the heavy atoms of a protein?

My aim is to calculate the contribution of conformational entropy to the ligand binding free energy. To do this, should I calculate the conformational entropy for the heavy or backbone atoms of the protein?

Thanks.