I figured it out myself. It seems like it's calles "OC30A" now. My energy minimization problems came from somewhere else and I have now been able to solve them. Excuse me for asking this, kind of obvious, question.
Simone ________________________________________ Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se]" im Auftrag von "Justin Lemkul [jalem...@vt.edu] Gesendet: Freitag, 17. April 2020 13:10 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] atomtype "OE" in charmm36 On 4/17/20 4:45 AM, Schirra, Simone wrote: > Dear Gromacs users, > > I want to simulate polyethylene glycol and I am using a script to build my > .itp and .gro files. The script is designed to work with charmm35r, however I > only found charmm36 available now (I read, that c35r was only temporary). I > thought, it should work with this version as well. > When I try energy minimization, the atomtype OE is not found. OE is used for > the ether oxygen's in the itp file. > I also found an ether toppar file at MacKerell Lab Hompage, however it seems > to be designed for use with charmm rather than gromacs. Which toppar file are you trying to use? > Is there a way to convert it for use with gromacs? Or is there another > definition I can use to work with my PEG? Or maybe c35r is still somewhere > around? C35r became C36 in official implementation. Likely the atom type just got renamed or assumed into an existing one, but without knowing which topology you're using, I can't comment. The PEO "toppar_ether" from Alex's site doesn't have anything called OE in it. -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. -- 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.
