How to include bound calcium in amylase structure

User discussions
1

GROMACS version:2025.3
GROMACS modification: No
I am new to MD. I am having trouble figuring out how to include a bound calcium in the calcium pocket of an alpha-amylase. I’ve renamed the the CA atom to CAL, as it’s called in CHARMM36. When I run pdb2gmx using CHARMM36, and TIP3p water model I get:

“Fatal error: Atom CA in residue CAL 0 was not found in rtp entry CAL with 1 atoms while sorting atoms.”

The Ca is in the pdb file as so:

…
ATOM 3557 CB ALA A 459 -13.378 26.982 -0.934 1.00 20.62 C
ANISOU 3557 CB ALA A 459 3949 819 3065 -291 -2313 450 C
TER
HETATM 3558 CA CAL A 501 6.664 -16.676 -11.359 1.00 6.86 CA
ANISOU 3558 CA CAL A 501 876 839 889 101 153 -70 CA
END

Is the calcium atom not annotated correctly in the pdb file? Do I need to add the calcium at a later step?

Thanks in advance

2

The atom name should be set to CAL, as well as the residue name.

3

Thanks for your reply!

I’ve changed it to the below, and I’m still getting the same error.

ATOM 3557 CB ALA A 459 -13.378 26.982 -0.934 1.00 20.62 C
ANISOU 3557 CB ALA A 459 3949 819 3065 -291 -2313 450 C
TER
HETATM 3558 CA CAL A 501 6.664 -16.676 -11.359 1.00 6.86 CAL
ANISOU 3558 CA CAL A 501 876 839 889 101 153 -70 CAL
END

and I’ve also tried

HETATM 3558 CAL CAL A 501 6.664 -16.676 -11.359 1.00 6.86 CAL
ANISOU 3558 CAL CAL A 501 876 839 889 101 153 -70 CAL

and I get:

“Fatal error: Atom CAL in residue CA 0 was not found in rtp entry CA with 1 atoms while sorting atoms.”

4

PDB is a fixed format; you’ve shifted the “CAL” residue name one column too far to the right, so only “CA” is being detected.

5

That’s fixed it, thanks! mdtutorials.com has also been a great resource, so thanks for that as well.