Hi, No it did not work!
In fact, I even copied DIHEDRAL entries from Galycam dat file and used same
spacing and format (just renamed atom names as I have in my ligand) but it
still prints SCNB and SCEE to 1.2 and 2.0 for those dihedrals.
$cat MORPH.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
DIHEDRAL
Ng-C -Cg-zz 1 0.25 0.0 3 SCEE=1.0
SCNB=1.0 Dimethylammonium
C -Cg-zz-du 1 0.25 0.0 3 SCEE=1.0
SCNB=1.0 N,N-Dimethyl amine
Hc-Cg-zz-du 1 0.25 0.0 3 SCEE=1.0
SCNB=1.0 N,N-Dimethyl amine
zz-Cg-C -O 1 0.20 0.0 3 SCEE=1.0
SCNB=1.0 Methyl propanoate
IMPROPER
NONBON
zz 0.0000 0.0000 ATTN, need revision
du 0.0000 0.0000 ATTN, need revision
$ grep -C 8 "SCNB" vacuum1.parm7
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 1.00000000E+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 1.00000000E+00
0.00000000E+00
You can see those 1.2 and 2.0 in last few entries.
regards,
Mish
On Wed, Dec 27, 2017 at 12:51 PM, Lachele Foley <lf.list.gmail.com> wrote:
> I kinda got lost. Did you get this to work? It looks like it worked, but
> maybe I misread/misunderstood.
>
> If not, there is an example frcmod on our site that has scee and scnb
> entries in it (see link after). If you haven't gotten things to work,
> maybe try loading that one as-is and/or using it as a template. Example
> frcmod:
> http://glycam.org/docs/forcefield/wp-content/uploads/
> sites/6/2016/03/frcmod.glycam06_intraring_doublebond_protonatedacids
>
> If you still need help, just say.
>
>
> On Tue, Dec 26, 2017 at 7:27 PM, mish <smncbr.gmail.com> wrote:
>
> > Not really. It loads the file well. To make sure, I put everything here:
> >
> > [mish.hok2 leaptest]$ cat MORPH.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
> >
> >
> >
> >
> >
> >
> >
> >
> > [mish.hok2 leaptest]$ cat leap.in
> >
> >
> > source leaprc.GLYCAM_06j-1
> >
> >
> > s = loadmol2 "./MORPH.mol2"
> >
> >
> > mod0 = loadAmberParams "./MORPH.frcmod"
> >
> >
> > saveAmberParm s "vacuum1.parm7" "vacuum1.rst7"
> >
> >
> > savepdb s "vacuum1.pdb"
> >
> >
> > quit
> >
> >
> > [mish.hok2 leaptest]$ tleap -f leap.in
> >
> >
> > -I: Adding /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/prep
> > to
> > search path.
> >
> >
> > -I: Adding /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/lib
> to
> > search path.
> >
> >
> > -I: Adding /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/parm
> > to
> > search path.
> >
> >
> > -I: Adding /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/cmd
> to
> > search path.
> >
> >
> > -f: Source leap.in.
> >
> >
> >
> >
> > Welcome to LEaP!
> >
> >
> > (no leaprc in search path)
> >
> >
> > Sourcing: ./leap.in
> >
> >
> > ----- Source:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > cmd/leaprc.GLYCAM_06j-1
> >
> >
> > ----- Source of
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > cmd/leaprc.GLYCAM_06j-1
> > done
> >
> >
> > Loading parameters:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > parm/GLYCAM_06j.dat
> >
> >
> > Reading title:
> >
> >
> > GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC 2011
> >
> >
> > Loading Prep file:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > prep/GLYCAM_06j-1.prep
> >
> >
> > Loading library:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > lib/GLYCAM_amino_06j_12SB.lib
> >
> >
> > Loading library:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > lib/GLYCAM_aminoct_06j_12SB.lib
> >
> >
> > Loading library:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > lib/GLYCAM_aminont_06j_12SB.lib
> >
> >
> > Loading library:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> lib/solvents.lib
> >
> >
> > Loading library:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > lib/atomic_ions.lib
> >
> >
> > Loading parameters:
> > /gwfefs/home/mish/soft/mysoft/amber-acs/amber16/dat/leap/
> > parm/frcmod.ionsjc_tip3p
> >
> >
> > Reading force field modification type file (frcmod)
> >
> >
> > Reading title:
> >
> >
> > Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> > JPCB (2008)
> >
> >
> > Loading Mol2 file: ./MORPH.mol2
> >
> >
> > Reading MOLECULE named LIG
> >
> >
> > Loading parameters: ./MORPH.frcmod
> >
> >
> > Reading force field modification type file (frcmod)
> >
> >
> > Reading title:
> >
> >
> > remark goes here
> >
> >
> > Checking Unit.
> >
> >
> > WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
> >
> >
> >
> >
> > -- ignoring the warning.
> >
> >
> >
> >
> > Building topology.
> >
> >
> > Building atom parameters.
> >
> >
> > Building bond parameters.
> >
> >
> > Building angle parameters.
> >
> >
> > Building proper torsion parameters.
> >
> >
> > Building improper torsion parameters.
> >
> >
> > total 3 improper torsions applied
> >
> >
> > Building H-Bond parameters.
> >
> >
> > Incorporating Non-Bonded adjustments.
> >
> >
> > Not Marking per-residue atom chain types.
> >
> >
> > Marking per-residue atom chain types.
> >
> >
> > (Residues lacking connect0/connect1 -
> >
> >
> > these don't have chain types marked:
> >
> >
> >
> >
> > res total affected
> >
> >
> >
> >
> > LIG 1
> >
> >
> > )
> >
> >
> > (no restraints)
> >
> >
> > Writing pdb file: vacuum1.pdb
> >
> >
> > Quit
> >
> >
> > [mish.hok2 leaptest]$ grep -C 8 "SCNB" vacuum1.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
> >
> >
> > [mish.hok2 leaptest]$
> >
> > On Wed, Dec 27, 2017 at 9:14 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> >
> > > (You can be sure you are loading the right file by messing it up to see
> > > if load fails.)
> > >
> > >
> > > On 12/26/17 4:12 PM, mish wrote:
> > > > 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
> > > >>>
> > > >> _______________________________________________
> > > >> AMBER mailing list
> > > >> AMBER.ambermd.org
> > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > >>
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 26 2017 - 20:19:13 PST
