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
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Received on Tue Dec 26 2017 - 20:00:02 PST
