Re: [AMBER] Calcium vdW parameters

From: Ken Merz <>
Date: Sat, 29 Nov 2014 08:07:38 -0500


 Manuel sent you info on Pengfei’s parameters. For calcium we have seen some issues because in solution the coordination number (CN) of water molecules to Ca(II) is 8, while in may proteins the CN is 6. This leads to the metal staying in the site, but typically it recruits an extra ligand or two to give a CN of 8. For the 12-6 parameters the HFE set gives a CN of ~7 and this might be your best bet. For the 12-6-4 potential the CN is 8 across the board. Let us know if any of these work for you. If not, Pengfei and I discussed trying to develop Ca(II) specific metal site binding parameters and if this interests you please contact us at and Good luck.


> On Nov 28, 2014, at 7:14 PM, Caitlin Scott <> wrote:
> Hi All,
> We have been performing simulations on an NMR structure of a
> calcium-binding protein, but the calcium ion does not remain coordinated
> to the carbonyls in the binding site. At the beginning of the production
> run, the protein conformation looks similar to the NMR state, but during
> the simulation, the distances between the calcium ion and carbonyls vary
> widely.
> To run AMBER MD, we are using the CHARMM 36 FF, whose files were generated
> with the CHARMM-GUI before using chamber to make the prmtop file. For the
> calcium ion, we're setting epsilon=-0.120 and Rmin/2=1.367 according to
> S. Marchand and B. Roux.
> We are concerned about LJ parameters for the calcium ion, but they seem
> accurate according to published references. Has anyone else run into
> similar problems simulating calcium ions in proteins?
> Caitlin Scott
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Sat Nov 29 2014 - 05:30:02 PST
Custom Search