Thanks so much to both of you. I understand the process now, but I would
really appreciate if you could you explain or point me toward a tutorial on
refitting charges on the CB carbon and its attached hydrogens via an RESP
fit? My plan is to calculate RESP charges for the entire modified residue,
and use use those charges for CB and the connected hydrogens, and then make
small adjustments to the hydrogen charges to ensure the total is an
integer.
Best,
Mish
On Tue, Nov 12, 2024 at 4:18 AM Dr. Anselm Horn via AMBER <amber.ambermd.org>
wrote:
> On 11/11/2024 08:52 PM, Carlos Simmerling via AMBER wrote:
> > when you run antechamber, you can use the -at flag to specify the atom
> type
> > source. "-at amber" should give you ff99SB atom types. This can be a good
> > place to start, but you still need to check them (and update to
> > ff14sb/ff99sb if desired), and I don't know of a way to use the
> > charges from ff99SB.
>
> I guess Carlos mentioned an important point:
> The atomic charges are a crucial part of the parameter set, and if you
> want your side chain analogs to be as similar as possible to the parent
> protein force fields, you may want to take this into account.
> But, ask Carlos indicated there is no "standard" way to obtain the
> necessary charges.
>
> You could e.g. use all charges from the parent forcefield from gamma
> position onward, and refit the CB and the hydrogens attached via an RESP
> fit to retain the major part of the original charges of the system.
> Maybe the sum of the atomic charges of C,O,N,H,CA, and HA is that small
> that a refit of just the hydrogen atoms attached to CB could be
> justified, yielding an even more parent-like charge set - or you could
> go the other direction, using more atoms for the refit and obtain an
> electrostatically "more balanced" system.
>
> Maybe this helps.
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-NÜrnberg (FAU)
> Germany
>
>
> >
> > On Fri, Nov 8, 2024 at 5:42 PM mish <smncbr.gmail.com> wrote:
> >
> >> Thank you! I am very clear on how I am going to get ff parameters for
> the
> >> small-molecule part.
> >>
> >> I am looking for advice on obtaining force-field parameters for all 18
> >> amino-acid side chains capped at CB but parameters same (or similar
> to) as
> >> for amino acids in ff19SB or ff14SB not in gaff.
> >>
> >> Best,
> >> Mish
> >>
> >> On Fri, Nov 8, 2024 at 4:30 PM Carlos Simmerling <
> >> carlos.simmerling.gmail.com> wrote:
> >>
> >>> if you're looking for small molecule parameters, I suggest trying
> >>> antechamber/gaff2. you might start here:
> >>> https://ambermd.org/tutorials/ForceField.php
> >>>
> >>> On Fri, Nov 8, 2024 at 5:12 PM mish <smncbr.gmail.com> wrote:
> >>>
> >>>> Thanks so much! I am sorry, I should have been more clear. I want
> Amber
> >>>> force field parameters for amino-acids capped at the Cb.
> >>>>
> >>>> Best,
> >>>> Mish
> >>>>
> >>>>
> >>>> On Fri, Nov 8, 2024 at 3:40 PM Carlos Simmerling <
> >>>> carlos.simmerling.gmail.com> wrote:
> >>>>
> >>>>> you might need to be more explicit in what you mean, since the
> >>>>> different protein force fields have different side chain parameters.
> do you
> >>>>> want a molecule that matches a particular force field and is just
> capped at
> >>>>> the CB, or do you want "good" small molecule parameters for
> molecules that
> >>>>> are amino acids analogs? For the latter, you might try GAFF2, but
> these
> >>>>> won't be the same parameters as those actually used in the amino
> acids. if
> >>>>> you want to former (a match to the protein model), you would need to
> do
> >>>>> more work, starting by picking which protein force field is your
> base.
> >>>>>
> >>>>> On Fri, Nov 8, 2024 at 3:40 PM mish via AMBER <amber.ambermd.org>
> >>>>> wrote:
> >>>>>
> >>>>>> Dear Amber community,
> >>>>>> I am looking for forcefield parameters of amino-acid analogs as
> those
> >>>>>> with where sidechains are capped by a hydrogen atom at Cβ. I want to
> >>>>>> use
> >>>>>> them to study amino-acid side chain interactions with come compounds
> >>>>>> and am
> >>>>>> looking for a reasonable mode of amino-acids that lacks backbone
> >>>>>> atoms. I
> >>>>>> will appreciate any suggestion to obtain reasonable parameters for
> such
> >>>>>> analogs.
> >>>>>>
> >>>>>> There are some studies (such as below) where authors used gromos.
> >>>>>>
> >>>>>> Anita de Ruiter, Bojan Zagrovic, Absolute binding-free energies
> between
> >>>>>> standard
> >>>>>> RNA/DNA nucleobases and amino-acid sidechain analogs in different
> >>>>>> environments, Nucleic Acids Research, Volume 43, Issue 2, 30 January
> >>>>>> 2015,
> >>>>>> Pages 708–718, https://doi.org/10.1093/nar/gku1344
> >>>>>>
> >>>>>> Thnks,
> >>>>>> Mish
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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> >
>
>
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Received on Tue Nov 12 2024 - 07:00:02 PST
