[gmx-users] Parametrization of Mn(ii) in charmm force field

[Justin Lemkul]

On 3/12/20 5:15 AM, Alessandra Villa wrote:
> Hi,
>
> You have to search in literature  for  parameters for Mn ions compatible
> with CHARMM36 and with the water model (some ions are parameterized to
> reproduce structural, thermodynamics, kinetic properties in water solution).
>
> For example Mn non-bonded parameters can be found *J. Phys. Chem. A* 2006,
> 110, 2, 691-699, but you should check if they are compatible with your
> setting

We have used parameters for Mn2+ from dx.doi.org/10.1021/jp309150r with 
some specific modifications for interactions with His residues given in 
the SI of one of our recent articles 
(https://aac.asm.org/content/aac/suppl/2017/10/13/AAC.01572-17.DCSupplemental/zac011176653s1.pdf)

-Justin

> Best regards
> Alessandra
>
>
> On Thu, Mar 12, 2020 at 5:26 AM Pranav BVN <prathegreat2204 at gmail.com>
> wrote:
>
>> Greetings,
>> I'm searching for a method to use Mn(ii) ions in a protein ligand
>> simulation using charmm-36 ff in gromacs. But I donot seem to get any entry
>> in ffnonbonded.itp in the charmm36-all-atom-ff directory. Is there any way
>> to run the simulation with Mn using charmm36? Is there any way to
>> achieve this?
>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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