Thanks a lot. I did try without the comma, without quotes etc.. but tleap
doesn't seem to pickup these numbers from frcmod file. Anyways, I will look
into it carefully if spacing or having number 000 is not the reason.
Best,
Sushil
On Tue, Dec 26, 2017 at 11:12 PM, David Cerutti <dscerutti.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Tue Dec 26 2017 - 16:30:02 PST
