[gmx-users] Calcium ions in GMXPBSA approch

[Mahboobeh Eslami]

Hi all GMX usersI hope you are wellI have simulated a protein-ligand complex. My protein has two calcium ions. I want to use GMXPBSA approach for free energy calculation. I have two question, please guide me:1- must I remove calcium ions in free energy calculation?2- If I remove calcium ions,  I will get following error in the first step of MMPBSA calculation:Fatal error:
Index[1673] 1676 is larger than the number of atoms in the
trajectory file (1675). There is a mismatch in the contents
of your -f, -s and/or -n files.Thank you so much