# How to include bound calcium in amylase structure

**URL:** <https://gromacs.bioexcel.eu/t/how-to-include-bound-calcium-in-amylase-structure/12958>\
**Category:** User discussions\
**Tags:** pdb2gmx\
**Created:** [November 20, 2025, 3:40pm UTC](https://gromacs.bioexcel.eu/t/how-to-include-bound-calcium-in-amylase-structure/12958 "2025-11-20T15:40:15Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![apara](https://avatars.discourse-cdn.com/v4/letter/a/71e660/32.png) [@apara](https://gromacs.bioexcel.eu/u/apara)\
**Post date:** [November 20, 2025, 3:40pm UTC](https://gromacs.bioexcel.eu/t/how-to-include-bound-calcium-in-amylase-structure/12958/1 "2025-11-20T15:40:15Z")

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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

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [November 20, 2025, 7:08pm UTC](https://gromacs.bioexcel.eu/t/how-to-include-bound-calcium-in-amylase-structure/12958/2 "2025-11-20T19:08:32Z")

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

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<div class="post-metadata">

**Author:** ![apara](https://avatars.discourse-cdn.com/v4/letter/a/71e660/32.png) [@apara](https://gromacs.bioexcel.eu/u/apara)\
**Post date:** [November 20, 2025, 7:30pm UTC](https://gromacs.bioexcel.eu/t/how-to-include-bound-calcium-in-amylase-structure/12958/3 "2025-11-20T19:30:49Z")

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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.”

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<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [November 21, 2025, 3:06am UTC](https://gromacs.bioexcel.eu/t/how-to-include-bound-calcium-in-amylase-structure/12958/4 "2025-11-21T03:06:14Z")

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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.

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<div class="post-metadata">

**Author:** ![apara](https://avatars.discourse-cdn.com/v4/letter/a/71e660/32.png) [@apara](https://gromacs.bioexcel.eu/u/apara)\
**Post date:** [November 21, 2025, 2:23pm UTC](https://gromacs.bioexcel.eu/t/how-to-include-bound-calcium-in-amylase-structure/12958/5 "2025-11-21T14:23:23Z")

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That’s fixed it, thanks! [mdtutorials.com](http://mdtutorials.com) has also been a great resource, so thanks for that as well.