On 6/4/14, 2:25 PM, elham tazikeh wrote:
Dear Justin Please ignore my previous questions. I want to do 2 md simulations: 1) protein and Cu, 2) protein and Zn. After checking force fields in gromacs 4.5.3, I found oplsaa in which there are both Cu and Zn ions in atomtype.atp file. Then I used gromacs 4.6.5 (with opls force field) to do md simulations. I added ions to my system using genion command. genion -s ions.tpr -o sol_ions.gro -p topol.top -pname CU -pq +2 -neutral -conc 0.025. genion -s ions.tpr -o sol_ions.gro -p topol.top -pname ZN -pq +2 -neutral -conc 0.025. In both cases, ions were added without problem. Then, I used grompp -f em.mdp -c sol_ions.gro -p topol.top -o em.tpr In case of protein and Cu, there is not problem. But, in case of protein and Zn, I encountered error: No such moleculetype ZN. I checked ions.itp in opls force field in gromacs 4.6.5, I found, there are both Cu and Zn ions in atomtype.atp file. But, there is only Cu in ions.itp file. How to do md simulation of protein-zn system using gromacs 4.6.5.
It may not be possible, but that's a force field issue, not a software issue. Most force fields don't cover more than a few metal ions, and even then the parameters for transition metals are generally incapable of capturing the true physical behavior of these ions. Such is the limitation of additive MM force fields.
The Zn parameters were indeed removed from OPLS; their parameters were either undocumented or found to be incorrect. So it is possible to use 4.5.3 to "make things work," but the parameters you're applying are not trustworthy.
-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.
