Look at the Glycam force field files--those SCEE and SCNB values are not
the defaults. It looks like the only difference with your frcmod may be
that there is a comma between SCEE=1.0 and SCNB=1.0 (the Glycam frcmod has
just blank space). See if you can engage the custom 1:4 scaling factors
with a sugar component in your system, to make sure that it's about the
frcmod and not something else you are doing or failing to do.
Dave
On Tue, Dec 26, 2017 at 3:09 AM, mish <smncbr.gmail.com> wrote:
> Dear all,
>
> I wonder if it should be possible to read SCNB and SCEE entries from
> frcmod file? I am using AmberTools16. Ligand is a modified GLYCAN and it
> has dummy atom. I want to keep SCNB and SCEE to 1.0. The frcmod loaded to
> tleap is in the following format:
>
> -----ligand.frcmod--------
> remark goes here
> MASS
> zz 0.000 0.000 ATTN, need revision
> du 0.000 0.000 ATTN, need revision
>
> BOND
> Cg-zz 0.00 0.000 ATTN, need revision
> zz-du 0.00 0.000 ATTN, need revision
>
> ANGLE
> C -Cg-zz 0.000 0.000 ATTN, need revision
> Cg-zz-du 0.000 0.000 ATTN, need revision
> Hc-Cg-zz 0.000 0.000 ATTN, need revision
>
> DIHE
> Ng-C -Cg-zz 1 0.000 0.000 0.000 SCEE=1.0,
> SCNB=1.0 ATTN, need revision
> C -Cg-zz-du 1 0.000 0.000 0.000 SCEE=1.0,
> SCNB=1.0 ATTN, need revision
> Hc-Cg-zz-du 1 0.000 0.000 0.000 SCEE=1.0,
> SCNB=1.0 ATTN, need revision
> zz-Cg-C -O 1 0.000 0.000 0.000 SCEE=1.0,
> SCNB=1.0 ATTN, need revision
>
> IMPROPER
>
> NONBON
> zz 0.0000 0.0000 ATTN, need revision
> du 0.0000 0.0000 ATTN, need revision
> ----------
>
> --leap.in--
> source leaprc.GLYCAM_06j-1
> loadAmberParams "./ligand.frcmod"
> s = loadmol2 "./liagnd.mol2"
> saveAmberParm s "ligand.parm7" "ligand.rst7"
> quit
> ---
>
> I wonder if it is possible to have scnb=scee=1 set to those dihedrals
> defined in frcmod file. Currently, leap set it those to default (last two
> entries in my case are 1.2 and 2.0):
>
> --parm7---
>
> %FORMAT(5E16.8)
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.20000000E+00 1.20000000E+00 0.00000000E+00
> 0.00000000E+00
> %FLAG SCNB_SCALE_FACTOR
> %FORMAT(5E16.8)
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 1.00000000E+00 1.00000000E+00 1.00000000E+00
> 1.00000000E+00
> 1.00000000E+00 2.00000000E+00 2.00000000E+00 0.00000000E+00
> 0.00000000E+00
> %FLAG SOLTY
> ----
>
> Sincerely,
> Mish
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Received on Tue Dec 26 2017 - 06:30:03 PST
