Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? from Lachele Foley on 2017-12-26 (Amber Archive Dec 2017)

From: Lachele Foley <lf.list.gmail.com>
Date: Tue, 26 Dec 2017 23:22:42 -0500

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.

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.

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...

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.

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
> > > > >>> 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
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> > > >
> > > _______________________________________________
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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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:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Dec 26 2017 - 20:30:02 PST