[gmx-users] Charges and Antechamber

[João Henriques]

This can potetially involve minimal editting or a lot of work. If you will
be using atom types already in place, you mainly need to edit the rtp file.
The charges, bonds and impropers go there. Other files need minimal work
like the residuetypes.dat and possibly the hdb, r2b, etc.

Avoid touching the original FF under share/gromacs/top. Make a copy of it
on your work directory and edit that one. Also, please don't take this task
lightly. Modifying a FF requires a good understanding of the task at hand.
Mistakes might become costly and may even go unnoticed while produce
wrong/false results.

João

On Oct 3, 2017 4:36 PM, "Sergio Manzetti" <sergio.manzetti at fjordforsk.no>
wrote:
>
> 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.henriques at gmail.com>
> To: "gmx-users" <gmx-users at 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.manzetti at 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.henriques at gmail.com>
> To: "gmx-users" <gmx-users at 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.manzetti at 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-request at 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-request at 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-request at 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-request at 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-request at gromacs.org.