On 8/26/19 12:04 PM, Edjan Silva wrote:
Dear users, I am trying to perform a simulation with a protein which contains two nickel atoms in the active site. When using the pdb2gmx command the following error appears: 'NI' not found in residue topology database I have edited the ions.itp file in the force field directory used (opls) but the same error still appears.
pdb2gmx does not read .itp files, it reads .rtp files. You need to add a residue definition there.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
