On 8/5/14, 5:01 AM, shahab shariati wrote:
Dear gromacs users. My system contains protein + ligand. Total charge of my protein = 0 My ligand has -NH2 group. I want to do 2 md simulations: 1)deprotonated state of ligand (-NH2). => Total charge of system= 0 2)protonated state of ligand and (-NH3+)=> Total charge of system=+1 I have no problem about the first simulation. I have a question about the second simulation: Should I one Cl ion to system using genion tool? I want to study effect of the charged ligand on the protein.
Yes, that would be considered standard procedure. -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.
