Dear Alan,
Yes, you can use ff19SB... but you have to make sure the other parameters/models are compatible with it... in the case of ff19SB, you should use OPC water model [
https://doi.org/10.1021/acs.jctc.9b00591]...
Protein-DNA interactions are the same of ff14SB as ff19SB uses the same non-bonded parameters...
As far as I know Alexey Onufriev is comparing the performance of bsc0 (and bsc1?) parameters in different water/ion models, it seems OPC is a reasonable choice to represent both internal and external ion atmospheres, while TIP3P seems to outperform OPC for representing the inner shell... but this is work in progress, he may be able to comment more on that...
In addition, there are updated ion parameters coming soon [
https://doi.org/10.1021/acs.jcim.0c01390][
http://archive.ambermd.org/202102/0139.html]
Hence the leap input should read:
source leaprc.protein.ff19SB
source leaprc.water.opc
source leaprc.DNA.bsc1
Best,
Matías
----- Mensaje original -----
De: "Alan" <alanwilter.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Lunes, 15 de Febrero 2021 4:45:30
Asunto: Re: [AMBER] multi source calls in tleap
Thanks guys for your answer. I don't think it's a bug but more like a
"protection" as you mentioned Matias.
And I'm aware those are old FF, I was just testing my old tutorials in
order to update them and I was concerned, but not tested yet, the
combination that Matias ended up showing in his example, would not work
anymore, but I guess it should work.
I could eventually look into the source code to know exactly what tleap is
doing but that's fine for the moment.
BTW, what about FF19SB instead of FF14SB?
Best wishes,
Alan
On Thu, 11 Feb 2021 at 14:53, Matias Machado <mmachado.pasteur.edu.uy>
wrote:
> Dear Alan,
>
> These feature is present since AMBER 16 or so (at leat that is the oldest
> version I've tied)...
>
> I don't think it is a bug, but Dave should certainly know better that me...
>
> I think it is some kind of safe-lock to prevent users from doing
> potentially wrong things... such as over-witting force fields...
>
> Indeed, oldff/leaprc.ff99SB and oldff/leaprc.ff99bsc0 load almost the same
> stuff, but for the bsc0 parameters of DNA.
>
> Hence the right way to load the force field is just "source
> oldff/leaprc.ff99bsc0"
>
> Anyway, as David mention, both the parameters and the way to load them are
> very old fashion...
>
> One proper way to do it at present is:
>
> source leaprc.protein.ff14SB
> source leaprc.water.tip3p
> source leaprc.DNA.bsc1
>
> Best,
>
> Matías
>
> PS: I'm stating to use "leaprc.water.opc" and OP3 (OPC3) water model,
> which is much better than TIP3P for the same price :-P
>
> ----- Mensaje original -----
> De: "David A Case" <david.case.rutgers.edu>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Lunes, 8 de Febrero 2021 11:50:07
> Asunto: Re: [AMBER] multi source calls in tleap
>
> On Sun, Feb 07, 2021, Alan wrote:
>
> >I've only noticed that now in ambertools 2020, perhaps that happened years
> >ago, but my tleap scripts used to have:
> >
> >source oldff/leaprc.ff99SB
> >...
> >source oldff/leaprc.ff99bsc0
>
> >Which now throws an error.
>
> Looks like a bug to me. I've submitted a fix for the upcoming
> AmberTools21.
> Thanks for the report.
>
> Is there a command to "unload" or "unsource" loaded parameters?
>
> No.
>
> >For now I've just broken my one script in several scripts, which is fine
> >but, still, it would be nice to know more about it.
>
> Just hoping here that you have a good reason to be using such outdated
> force
> fields.
>
> ...dac
>
>
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>
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>
--
Alan Silva 🚲🏊♂🏃♂🇧🇷🇫🇷🇬🇧
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Received on Mon Feb 22 2021 - 11:30:03 PST
