Re: [gmx-users] atomtype "OE" in charmm36
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.
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.
[gmx-users] atomtype "OE" in charmm36
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. 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? I would be very grateful if someone could help me! Simone -- 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.
