# Ca2+ binding protein

**URL:** <https://gromacs.bioexcel.eu/t/ca2-binding-protein/679>\
**Category:** User discussions\
**Created:** [August 17, 2020, 9:02pm UTC](https://gromacs.bioexcel.eu/t/ca2-binding-protein/679 "2020-08-17T21:02:13Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Bin](https://avatars.discourse-cdn.com/v4/letter/b/edb3f5/32.png) [@Bin](https://gromacs.bioexcel.eu/u/Bin)\
**Post date:** [August 17, 2020, 9:02pm UTC](https://gromacs.bioexcel.eu/t/ca2-binding-protein/679/1 "2020-08-17T21:02:13Z")

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Hello all,

I am working on a 50 ns MD simulation on Ca2+ binding protein using the charmm27 force field. MD simulation results show that Ca2+ cannot be stable in the Ca2+ binding site during 40 -50 ns time period.

The note below is what I got:

NOTE 1 [file topol.top, line 49]:  
In moleculetype ‘Ion\_chain\_A2’ 2 atoms are not bound by a potential or  
constraint to any other atom in the same molecule type…

Also, I am not sure if “tc-grps” for MD simulation is set up correctly.  
tc-grps = Protein\_CA NA\_CL\_Water

Could you please give me some suggestions on my problem?

Thank you very much,

Bin

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**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:** [August 18, 2020, 12:31am UTC](https://gromacs.bioexcel.eu/t/ca2-binding-protein/679/2 "2020-08-18T00:31:13Z")

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> [@Bin](#):
>
> I am working on a 50 ns MD simulation on Ca2+ binding protein using the charmm27 force field. MD simulation results show that Ca2+ cannot be stable in the Ca2+ binding site during 40 -50 ns time period.

Use the latest CHARMM36 force field, which includes NBFIX terms for Ca2+:carboxylate interactions. Divalent ions are notoriously difficult to model properly in nonpolarizable force fields.

> [@Bin](#):
>
> NOTE 1 [file topol.top, line 49]:  
> In moleculetype ‘Ion\_chain\_A2’ 2 atoms are not bound by a potential or  
> constraint to any other atom in the same molecule type…

This is likely unimportant.

> [@Bin](#):
>
> Also, I am not sure if “tc-grps” for MD simulation is set up correctly.  
> tc-grps = Protein\_CA NA\_CL\_Water

This is how I would do it.

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**Author:** ![Bin](https://avatars.discourse-cdn.com/v4/letter/b/edb3f5/32.png) [@Bin](https://gromacs.bioexcel.eu/u/Bin)\
**Post date:** [August 18, 2020, 1:04am UTC](https://gromacs.bioexcel.eu/t/ca2-binding-protein/679/3 "2020-08-18T01:04:57Z")

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Thank you very much for your suggestions, Justin. I will try CHARMM36 force field.