Hello Lachele,
thank you very much for your complex information !
Best wishes,
Marek
Dne Sun, 05 Nov 2017 11:34:59 +0100 Lachele Foley <lf.list.gmail.com>
napsal/-a:
> 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/
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >
>> >
>> >
>>
>>
>> --
>> Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
--
Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 05 2017 - 16:30:02 PST
