On 3/16/14, 9:49 AM, Andrew Bostick wrote:
Dear Kalyan Thanks for your reply I want to use Zn2+ ions with my protein. There is Zn2+ ions in atomtypes.atp file of opls force field. But there is not Zn2+ ions in ions.itp file of of opls force field. Based on your answer, now, I can not use Zn2+ ions in genion tool. Is it true? But I used genion -s ions.tpr -o mol.gro -p topol.top -np 2 -pname ZN -pq +2 and I did not encountered with error and solvent molecules replaced with Zn2+ ions. I confused. Please give me more explanations.
genion does not read ions.itp to understand which ions it can and can't add. It does what you tell it. You can name your monovalent ions anything you like at this stage; the only thing that matters is that the name supplied corresponds to some known [moleculetype] in that force field - either in ions.itp or in an .itp file of your own creation. If there is no ZN [moleculetype] anywhere, grompp will die with a fatal error.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
