Before going further: these are just our recommendations. if the geometry
of the linkage is very important to you, then you really need to validate
whatever you choose. If it is being held more-or-less still (binding site,
other sterics, etc.), then it might not be a big deal either way. To
validate, try to find info about the linkage geometries from some
corresponding experimental source (NMR is usually good), and see if the
simulation gives similar observables. Do be careful to compare the
observations (if NMR, then NOEs, J-counplings, etc) and not the conclusions
(if NMR, populations of angles derived from J-couplings and such).
So, that said: yes, we generally at least start with the glycam values for
anything that is half or more on the 'glycam side' of things. Anything
that has more gaff character than glycam character might do well with gaff
parms. We do tend to apply scee=scnb=1 to anything touching glycam, but
there certainly might be situations where that is not ideal.
On Sat, Nov 4, 2017 at 10:07 AM, Marek Maly <marek.maly.ujep.cz> wrote:
> Thanks Lachele !
>
> I saw the scee, scnb records in Glycam ff file, but
> since such records are not present in GAFF or probably
> any f the Amber ff, I was thinking that those are just comments.
>
> It is nice that it is possible to include those parameters in frcmod and
> would be appropriate to mention it in Amber manual and in the
> description of frcmod format http://ambermd.org/formats.html#frcmod .
>
> Regarding decision between the #1 and #2 I was thinking that
> both are in principle possible but that it is always a good idea to use
> appropriate scaling factors.
>
> So as I understood well, in your opinion and according your experiences #2
> (Glycam substitution) is a bit more suitable and this also holds probably
> (to be consistent) also
> for the remaining parameters like bond/angle (e.g. c3-Os, c3-Os-Cg ...)
> am I right ?
>
> Best wishes,
>
> Marek
>
>
>
> Dne Sat, 04 Nov 2017 11:02:38 +0100 Lachele Foley <lf.list.gmail.com>
> napsal/-a:
>
> > I think these are your questions. Please correct me if I missed or
> > misunderstood anything.
> >
> > 1. You want to know which numerical values to assign to the scaling
> > factors (scee and scnb) for dihedrals at the border between gaff and
> > glycam.
> >
> > 2. You want to know where to put those numbers so that they are
> > reflected
> > in the prmtop file and in the simulation.
> >
> > Answers:
> >
> > 1. Current opinion from a member of the group with gaff/glycam
> > experience
> > is to use similar glycam torsions if present and use glycam scaling (no
> > scaling, scee=scnb=1).
> >
> > 2. The values are set in the 'comments' in the parameter or frcmod file.
> > Everything except the "SCEE=" and "SCNB=" parts are treated as comments,
> > but those entries are read. See the link below for an example of a
> > frcmod
> > file employing this.
> >
> > http://glycam.org/docs/forcefield/wp-content/uploads/
> sites/6/2016/03/frcmod.glycam06_intraring_doublebond_protonatedacids
> >
> > For more glycam param examples: http://glycam.org/params
> >
> >
> > On Fri, Nov 3, 2017 at 6:28 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> >
> >> Hello,
> >>
> >> I plan to simulate polymers decorated with (covalently bound) Glucose
> >> so I
> >> would like
> >> to use GAFF for the polymer part and the GLYCAM for the sugar (I am
> >> using
> >> Amber16).
> >>
> >> Since Glucose is covalently bound to the polymer part, it is clear that
> >> on the "border" of that 2 parts (polymer/sugar) which I would like to
> >> simulate using different
> >> force fields, I will have some mixed GAFF-GLYCAM terms (bond, angle,
> >> dihedral).
> >>
> >> Lets assume this concrete mixed GAFF-GLYCAM dihedral term:
> >>
> >> c3-c3-Os-Cg
> >>
> >> One has to decide if to treat it (use the relevant torsional parameters)
> >> in frcmod file
> >> as the:
> >>
> >> #1 GAFF dihedral
> >> so in frcmod file will be present line:
> >>
> >> c3-c3-Os-Cg 3 1.150 0.000 3.000
> >> (numbers corresponding to GAFF term X -c3-os-X )
> >>
> >> OR
> >>
> >> #2 GLYCAM dihedral
> >> so in frcmod file will be present line:
> >>
> >> c3-c3-Os-Cg 1 0.16 0.0 3.
> >> (corresponding to Cg-Os-3C-CT or Cg-Os-3C-CX GLYCAM terms)
> >>
> >>
> >> After we choose between the #1, #2 dihedral term implementation would be
> >> probably a good idea also to set adquate 1-4 scaling factors for this
> >> mixed dihedral term ( c3-c3-Os-Cg ) "scee" and "scnb".
> >>
> >> i.e. scee = 1.2, scnb = 2.0 in case #1 and scee = 1.0, scnb = 1.0 in
> >> case
> >> #2.
> >>
> >> The problem is that I am not able to find the way, how set individually
> >> (
> >> i.e. for the concrete
> >> dihedral term/s ) the "scee" and "scnb" parameters.
> >>
> >> It would be the best to have the possibility to set this in the given
> >> frcmod file,
> >> but this, as far as I know, is not possible, and the eventual
> >> possibility
> >> to correct
> >> scaling 1-4 parameters for the given dihedral term/s already in PRMTOP
> >> file (i.e. by using ParmEd) I did not find as well.
> >>
> >>
> >> So my questions are:
> >>
> >> A) Is there any way how to set in this individual manner 1-4 scaling
> >> factors ?
> >>
> >> B) I suppose that in case of systems simulated using two force fields
> >> which differ in scee and scnb scaling parameters, Amber puts in PRMTOP
> >> file proper scee and scnb values which correspond to the given force
> >> filed
> >> (i.e. relevant atom types). But what scee/scnb values is used in such
> >> mixed terms like c3-c3-Os-Cg ? I suppose that it might be the default
> >> values i.e.: scee = 1.2, scnb = 2.0 so if there is no way how to set
> >> "manually" 1-4 scaling factors for the individual dihedral terms, there
> >> is a still possibility to subordinate the choice between the #1 and
> >> #2
> >> to the default values of scee and scnb parameters. Am I right ?
> >>
> >> Thanks in advance for relevant comments,
> >>
> >> Best wishes,
> >>
> >> Marek
> >>
> >>
> >>
> >>
> >> --
> >> Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
>
> --
> Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/
>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sun Nov 05 2017 - 03:00:02 PST
