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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Received on Fri Nov 03 2017 - 15:30:03 PDT
