yes, the ions I have can be considered as bound. I found out I also had to declare the type of residue as "Ion" in file residues.dat :)
On Fri, Jun 23, 2017 at 4:44 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 6/23/17 3:50 PM, Jose Borreguero wrote: > >> Dear Gromacs users, >> >> I'm trying to add a new type of atom as an ion. Looking at already >> existing >> ions, such as sodium (NA), I see there's an entry both in files ions.itp >> and aminoacids.rtp. My question is, what is the rationale of declaring >> ions >> both as ions and as residues? Is this always required? >> >> > If you want to process it with pdb2gmx, you need an entry in an .rtp > file. If you just have an ion that you're going to add into a box, you can > rely on ions.itp. The current implementation covers both cases. Some > structures have bound ions and it makes life easier to be able to process > them with pdb2gmx. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > 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. > -- 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.
