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
[email protected] | (410) 706-7441
==================================================
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