[gmx-users] Potential energy of a single amino acid residu

Tom Venken tom.venken at student.kuleuven.be
Tue Mar 10 11:44:51 CET 2009


I am trying to calculate the potential energy of an individual amino  
acid and its interaction energy with the rest of the protein. I have  
found another user with a similar problem:  
so I tried to follow the same procedure. An index-file was made  
containing a group with the specific residu (r_8 in this case) and a  
group of the rest of the protein without this residu (Protein_&_!r_8).  
The mdp-file was changed as well, now containing:
energygrps                                =    r_8
energygrps_excl                           =    Protein_&_!r_8 non-Protein
so basically only the energy of r_8 would be calculated with the  
following commands:
grompp -f ppmd_r8.mdp -c mdwater.pdb -p topol.top -o topol_md_r8.tpr  
-t traj_mdwater.trr -n r8.ndx
mdrun -s topol_md_r8.tpr -c md_r8.pdb -e ener_md_r8.edr -rerun  
traj_md.trr (thus feeding the trajectory again but now with the new  
then g_energy -f ener_md_r8.edr -s topol_md_r8.tpr -o Epot_r8.xvg
Unfortunately the output still gives me the energy of the whole  
protein and not of the specific residu. Any idea of what went wrong?

Thanks in advance,


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