[gmx-users] different number of charges and atoms of ligand in free energy calculation

[Sadaf Rani]

Dear Gromacs users
I am simulating the free energy of binding of a ligand with protein using
the dual topology method. I am getting the following message in log file:-

*There are 28 atoms and 29 charges for free energy perturbation*
I have 27 atoms in ligand plus two Na+ ions, It should give an equal number
of atoms and charges as per my understanding.

Could anyone please suggest me where I am committing any mistake? I will be
really thankful.

Thanks in advance.

Sadaf

Ph.D. visiting student
Lancaster University Uk.