yes we will follow up on that separately. there are indeed differences
between ff12SB and 14SB, and while we think 14SB is improved, I'm always
enthusiastic about seeing quantitative validation. thanks!
On Tue, Jun 14, 2016 at 9:41 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi Carlos,
>
> Thanks for the clarification ... It would be great if you or your
> co-worker(s) could clarify in a detailed exchange off the list with
> Miroslav the differences in his results between ff12SB and ff14SB to
> make sure that the force field implementation is actually working as it
> should ... And once this is clarified, an update to the list would be
> great.
>
> Greetings
> Vlad
>
> On 06/14/2016 03:17 PM, Carlos Simmerling wrote:
> > hi all,
> > sorry for the delayed response, I was on the road. I've checked on this
> and
> > what's going on here is that these atoms should indeed be CT, not 2C. The
> > manuscript table was incorrect, we listed them all as 2C but should be
> CT.
> >
> > The main point here is that the 4-atom combination is unique, so it
> didn't
> > matter if they are 2C or CT. Both have the same vdw and other atomic
> > parameters. Using 2C for the others allowed us to change them
> independently
> > of some situations that had CT. For Phe and Tyr I think these are already
> > independent so it didn't matter. Keeping CT had the advantage that it
> > didn't change the alphabetical order for the impropers (as has been
> covered
> > in separate threads), so didn't change the improper energy.
> >
> > As far as I can tell the only issue here is that the article lists 2C
> > instead of CT, but this doesn't impact the parameters in any way. They
> were
> > fit using CT.
> >
> > Please respond back to this thread if you see something that we have
> > missed...
> > Carlos
> >
> > On Tue, Jun 14, 2016 at 8:53 AM, Vlad Cojocaru <
> > vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> >
> >> Well, it seems to me that in the aminoct12.lib file which is loaded by
> >> leaprc.ff14SB, the CB atom of PHE and TYR has a CT type and not 2C as
> >> should be based on the paper (Maier et al, supporting info). Unless I am
> >> missing something, this is a very unfortunate mistake that was not
> >> spotted by anybody till now although ff14SB is in use for a while now.
> >> The more puzzling thing is the difference to ff12SB because the
> >> leaprc.ff12SB loads exactly the same libraries, so there shouldn't be
> >> differences between ff12SB and ff14SB (they both load CB in TYR and PHE
> >> as CT type)...
> >>
> >> If I am not wrong and the error is in the libraries, it brings up the
> >> importance of some sort of automated check of the topologies created.
> >> Something like a log file with all parameters per residue type present
> >> in the created topology in an easy-to-read format that can be consulted
> >> after the creation of a topology file ... I know parmed has the
> >> functionality to check topologies but still requires users to define
> >> which parameters they would like to check .... Moreover, some automatic
> >> checks with warnings could be useful when new versions of ff are
> >> implemented. .. For example atoms types 2C, 3C, are specific for ff14SB
> >> ...Upon creating a topology file, there could be an automated check
> >> script for these atom types and if they are not present where they
> >> should be, a warning could be issued ....
> >>
> >> Best
> >> Vlad
> >>
> >>
> >> On 06/14/2016 02:04 PM, David A Case wrote:
> >>> On Fri, Jun 10, 2016, Miroslav Krepl wrote:
> >>>> I have a question regarding the ff14SB protein ff (the recommended
> >>>> default) as implemented in AMBER. In some of my systems, it
> >>>> seems to me that I am getting better results for tyrosine and
> >> phenylalanine
> >>>> using the preliminary ff12SB
> >>>> version.
> >>>>
> >>>> It almost looks to me as if the new atom type describing the
> >>>> phenylalanine and tyrosine CB atom (type 2C) was not implemented in
> the
> >>>> residue files at all. There is discrepancy between the AMBER
> >> implementation
> >>>> and the original literature describing the ff14SB.
> >>>>
> >>>>
> >>>> As a result, I observe in simulations that the phenylalanine and
> >>>> tyrosine behave in ff14SB similarly as with ff99SB. Their chi2
> dihedral
> >>>> profiles appear to be similar. The same issue is not present with the
> >>>> ff12SB force field version which works differently and in my systems
> >>>> better.
> >>> Thanks for the report. We are looking into the origins of the behavior
> >> you
> >>> report, and will post something here as soon as we can. This email is
> >> just a
> >>> place-holder to indicate that we have not forgotten about your mail.
> >>>
> >>> ....regards...dac
> >>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> --
> >> Dr. Vlad Cojocaru
> >> Computational Structural Biology Laboratory
> >> Department of Cell and Developmental Biology
> >> Max Planck Institute for Molecular Biomedicine
> >> Röntgenstrasse 20, 48149 Münster, Germany
> >> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >> http://www.mpi-muenster.mpg.de/43241/cojocaru
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru
>
>
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Received on Tue Jun 14 2016 - 07:00:03 PDT
