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
>
>
>
>
> --
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>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Sat Nov 04 2017 - 03:30:02 PDT
