[gmx-users] Insertion of chromium III ion into lipid bilayer

[Justin Lemkul]

On 10/19/13 10:27 AM, Sathya wrote:
> Hi,
>
>      I want to add chromium III ion into lipid bilayer.  I have included cr
> entry in the ions.itp file,  and I used grompp it shows error like Atom
> types cr+3 is not found. After removing cr ions from the ions.itp file it
> works and after using genion to add cr3+ ions into lipid the following
> command was used.
>
>                       genion -s ions.tpr -o dppc_solv_ions.gro -p topol.top
> -pname CR -pq 3
>
> But it shows ""No ions to add and no potential to calculate.. ""
> Is it necessary to include chromium entry in the ions.itp file?  What file i
> should modify to add cr into lipid?
> Please explain me to solve this..
>

Entries in ions.itp are dependent upon those atom types actually existing in the 
force field.  If the Cr(III) ion has not been parametrized for your force field 
(which is unlikely to be true for any of the force fields in Gromacs), then 
there's not much you can do besides derive the parameters yourself.  I seriously 
doubt that any additive biomolecular force field will adequately represent a 
transition metal like Cr.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================