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.
[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.
Re: [gmx-users] PEG from ATB: No residues in chain
Yes, there is no protein/DNA/RNA in my system. Do I have to define this somewhere? I get the warning when executing pdb2gmx. -Ursprüngliche Nachricht- Von: gromacs.org_gmx-users-boun...@maillist.sys.kth.se Im Auftrag von Alessandra Villa Gesendet: Mittwoch, 4. März 2020 17:26 An: gmx-us...@gromacs.org Betreff: Re: [gmx-users] PEG from ATB: No residues in chain Hi, On Wed, Mar 4, 2020 at 4:11 PM Schirra, Simone wrote: > Dear Gromacs users, > > I'm totally new to GROMACS and I want to simulate a PEG chain in > different environment. I found various PEG topologies on the ATB > website and tried to use them combined with the force field provided > on the website. However, I always get a warning like this: > > "Warning: No residues in chain starting at YAHE identified as > Protein/RNA/DNA. > This makes it impossible to link them into a molecule, which could > either be correct or a catastrophic error. Please check your > structure, and add all necessary residue names to residuetypes.dat if > this was not correct." > > The warning says that you have no Protein/RNA/DNA residues and indeed PEG is polyethylene glycol. Or do you have also protein/DNA/RNA in the system? Is YAHE the molname given to PEG in the topology file? Where do you get the warning? Best regards Alessandra I have tried different topologies, the residues are always named > differently but they are never defined, although I use the force field > that ATB specifies for this. > Also in other databases I could only find PEG with other residues, but > not somewhere defined. Since it is a well known polymer, I guess that > it's well defined somewhere and I just need to know the correct name > for a r2b file or something like that... > I would be very grateful if someone could help me with this! > > 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. > -- 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.
[gmx-users] PEG from ATB: No residues in chain
Dear Gromacs users, I'm totally new to GROMACS and I want to simulate a PEG chain in different environment. I found various PEG topologies on the ATB website and tried to use them combined with the force field provided on the website. However, I always get a warning like this: "Warning: No residues in chain starting at YAHE identified as Protein/RNA/DNA. This makes it impossible to link them into a molecule, which could either be correct or a catastrophic error. Please check your structure, and add all necessary residue names to residuetypes.dat if this was not correct." I have tried different topologies, the residues are always named differently but they are never defined, although I use the force field that ATB specifies for this. Also in other databases I could only find PEG with other residues, but not somewhere defined. Since it is a well known polymer, I guess that it's well defined somewhere and I just need to know the correct name for a r2b file or something like that... I would be very grateful if someone could help me with this! 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.
