Getting fatal error for hetero atom

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1

GROMACS version:2020.5
GROMACS modification: Yes/No
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Hi I am getting fetal error message as below when I prepare topology for my protein
“Fatal error:
Atom CA in residue CA 1 was not found in rtp entry CA with 68 atoms
while sorting atoms”
I ran it in CHARMM36-feb2021 version
Could you please help me to solve this error? I have two CA in my protein

2

Hi,
CA is not a standard protein residue name. You can check if resname CA is defined in the force field tpr file or you can check if the name in the coordinate file is correctly given.
Best regards
Alessandra

3

Thank you for the reply. The Calcium ion is not defined in the .tpr file, I tried to include the topology of the Calcium as a separate line and ran the simulation but I got error that CA is not defined. I do not know exactly how to edit the topology file with 2 of my Ca2+ ions. Could you help me with that?

4

Hi,
I think the problem is that CA is not the atom name for Calcium in CHARMM force field, but for a aromatic carbon.
The atom name for Calcium is CAL and the resname is CA
(see ions.itp in the force field directory)
I hope it helps
Alessandra

5

Thank you for the suggestion