Ca2+ binding protein

[Bin]

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

[jalemkul]

@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.

[Bin]

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