I am sorry but any personal email to you (lf.list_at_gmail.com) is bouncing
back from Gmail with the message "Address not found Your message wasn't
delivered to if.list.gmail.com because the address couldn't be found, or is
unable to receive mail. Can I send it to your UGA email on the web ?
Best,
Mish
On Wed, Dec 27, 2017 at 1:42 PM, Lachele Foley <lf.list.gmail.com> wrote:
> But, two of them are 99. So, they *are* being read, just not always when
> you want.
>
> Like in this line:
> 9.90000000E+00 2.00000000E+00 2.00000000E+00 9.90000000E+00
> 0.00000000E+00
>
> When you send the separate info, I'll try to figure it out. I've spent
> lots of time looking at these files...
>
>
> On Tue, Dec 26, 2017 at 11:36 PM, mish <smncbr.gmail.com> wrote:
>
> > On Wed, Dec 27, 2017 at 1:22 PM, Lachele Foley <lf.list.gmail.com>
> wrote:
> >
> > > Are you certain that those two are part of the ones that should have
> 1.0
> > as
> > > the scaling factor? Or, alternately, are you certain that all entries
> > > should have that scaling factor? Leap can also re-order things
> > sometimes,
> > > so the atom order in your input file might not be the same as in the
> > prmtop
> > > file.
> >
> >
> > I am quite sure that %FLAG SCEE_SCALE_FACTOR and %FLAG SCNB_SCALE_FACTOR
> > are the entries that shoudl have scaling factors. They differ when I
> > prepare ligand using GAFF or GLYCAM.
> >
> > Many things other than scee/scnb readings can go wrong. For example, you
> > > list four dihedrals above. But, the top file contains 35 dihedral
> > > entries. So, your system contains other things. And, if any of those
> > > dihedrals are doubly-specified (for example in your file and in a
> protein
> > > file), then the order in which they are read will determine which gets
> > > used.
> > >
> >
> > Other dihedrals are standard one from GLYCAM. I source
> leaprc.GLYCAM_06j-1
> > from those.
> >
> > >
> > > A better troubleshooting might be to use entries like this:
> > >
> > > DIHEDRAL
> > > Ng-C -Cg-zz 1 0.99 0.0 3 SCEE=9.9
> > > SCNB=9.9 Dimethylammonium
> > > C -Cg-zz-du 1 0.99 0.0 3 SCEE=9.9
> > > SCNB=9.9 N,N-Dimethyl amine
> > > Hc-Cg-zz-du 1 0.99 0.0 3 SCEE=9.9
> > > SCNB=9.9 N,N-Dimethyl amine
> > > zz-Cg-C -O 1 0.99 0.0 3 SCEE=9.9
> > > SCNB=9.9 Methyl propanoate
> > >
> > > Because nothing else (that I know of....) uses 9.9 as a scaling factor,
> > so
> > > you can easily see what came from your file. Note that I also changed
> > the
> > > entry value to 0.99 for similar reasons. Of course, for the final
> files,
> > > change it back...
> > >
> > >
> > I used 9.0, and till two of themare 1.2 and 2.0.
> >
> > $grep -C 10 "SCNB" vacuum1.parm7
> > %FLAG SCEE_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
> > 9.90000000E+00 1.20000000E+00 1.20000000E+00 9.90000000E+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
> > 9.90000000E+00 2.00000000E+00 2.00000000E+00 9.90000000E+00
> > 0.00000000E+00
> > 0.00000000E+00
> > %FLAG SOLTY
> >
> >
> >
> >
> > > Can you send me the actual input files and all commands? I won't share
> > > them, but I will probably share on this list general info about the
> fix.
> > >
> >
> > I am seding you a PM.
> >
> > Regards,
> > Mish
> >
> > >
> > >
> > > On Tue, Dec 26, 2017 at 11:10 PM, mish <smncbr.gmail.com> wrote:
> > >
> > > > 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
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> > > > > > > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >>>
> > > > > > > >> _______________________________________________
> > > > > > > >> AMBER mailing list
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> > > > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > >>
> > > > > > > > _______________________________________________
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> > > > > > >
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
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> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > > _______________________________________________
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> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > :-) Lachele
> > > > > Lachele Foley
> > > > > CCRC/UGA
> > > > > Athens, GA USA
> > > > > _______________________________________________
> > > > > AMBER mailing list
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> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
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> > > >
> > >
> > >
> > >
> > > --
> > > :-) 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 26 2017 - 21:00:05 PST
