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

[Justin Lemkul]

On 9/30/19 12:43 PM, sunyeping wrote:
> 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.

What you want is CAL, not CAD, for both the residue and atom name. From 
atomtypes.atp:

    CAD    112.41100 ; cadmium (II) cation
    CAI     12.01100 ; aromatic C next to CPT in trp
    CAL     40.08000 ; Calcium Ion

-Justin

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Justin A. Lemkul, Ph.D.
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