[gmx-users] How to handle calcium ions with charmm36 force field

[sunyeping]

Dear everyall,

I am trying to do simulations with a protein cotaining calcium ions. When I preprocess the pdb file for the structure with: 
    gmx pdb2gmx -f protein_ca_ligW_0.pdb -o protein.gro

I get the following error:
Fatal error:
Atom CA in residue CA 515 was not found in rtp entry CA with 68 atoms
while sorting atoms.

I checked the  atomtypes.atp file in the charmm36 force field directory and found that the calcium ion seems to be name CAD instead of CA, so I change the calcium atom name from "CA" to "CAD" and run the pdb2gmx command again.  This time I got the similar error:
Fatal error:
Atom CAD in residue CA 515 was not found in rtp entry CA with 68 atoms
while sorting atoms.

Now I don't know how to deal with this problems. Could anyone help me? 
Thanks in advance.

Yesping Sun