Thanks, in which file do you add your residue, do you have an example? Thanks!
Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "João Henriques" <joao.m.a.henriq...@gmail.com> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Tuesday, October 3, 2017 4:33:55 PM Subject: Re: [gmx-users] Charges and Antechamber I just left work and I'm terrible with typing on the phone, so please bear with me. Since I mostly work with proteins and modified residues it was always worth it for me to edit the actual FF instead of making an itp by hand. This way I let pdb2gmx do the tedious work of building the topology for myself. I simply give it a structure and it does its magic. Is it less work? Probably not, since editing a FF is not exactly the simplest of tasks and requires a lot of attention and knowledge about what is where in the many files that come in a FF folder. Still, I find it to have more pros than cons. To summarize, I don't build the topology. I add my custom residue to the FF and let pdb2gmx figure the rest out. Hope it made sense, Cheers, João On Oct 3, 2017 3:53 PM, "Sergio Manzetti" <sergio.manze...@fjordforsk.no> wrote: Thanks Joao, I am on the way with the QM part, but making the topology for GMX is a little bit more complicated. I thought of generating one with ANTECHAMBER Of a neutral species, then edit the topology itp file manually, but the propers are quite complex to re-edit. How did you get around this part? Sergio Manzetti [ http://www.fjordforsk.no/logo_hr2.jpg ] [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ | ] Midtun 6894 Vangsnes Norge Org.nr. 911 659 654 Tlf: +47 57695621 [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ | FAP ] From: "João Henriques" <joao.m.a.henriq...@gmail.com> To: "gmx-users" <gmx-us...@gromacs.org> Sent: Tuesday, October 3, 2017 3:50:55 PM Subject: Re: [gmx-users] Charges and Antechamber Hi! If your goal is to generate the atomic partial charges for a new residue/molecule (not existing in the FF you are interested in using), then doing the QM calculations is a must in most cases. For example, AMBER FFs have a well documented and specific recipe you can easily follow, which involves deriving the electrostatic potential from QM calculations at a specific level of theory + basis sets and then using the RESP fit procedure. Cornell, Wendy D., et al. "A second generation force field for the simulation of proteins, nucleic acids, and organic molecules." Journal of the American Chemical Society 117.19 (1995): 5179-5197. I've done this a couple of times and it was relatively simple. I never needed to use antechamber for anything else, all modelling and assignment of atom types were done manually. Exotic species might make things more complicated. P.S.: For non-AMBER FFs you need to follow their own recipes/methods. For example, GROMOS FFs don't have a fixed recipe for obtaining the charges (you can even set them by hand according to your own whim), but the calculations must reproduce solvation enthalpies, etc. In sum, check the original literature on the FF you plan on using to understand how to calculate your own charges in a way that respects that specific FF's "philosophy". Hope it helps, João On Tue, Oct 3, 2017 at 3:16 PM, Sergio Manzetti < sergio.manze...@fjordforsk.no> wrote: > Hi, I was wondering what the best approach is to simulate a negatively > charged topology imported from ANTECHAMBER (which can't do integral > charges): > > 1. Do QM calculations on the molecule, then edit the output from > Antechamber > > or > > 2. Do something else. > > Sergio Manzetti > > [ http://www.fjordforsk.no/logo_hr2.jpg ] > > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ > | ] > Midtun > 6894 Vangsnes > Norge > Org.nr. 911 659 654 > Tlf: +47 57695621 > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | > Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ > http://www.phap.no/ | FAP ] > > -- > 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? 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