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
>
>
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Received on Tue Dec 26 2017 - 16:30:03 PST
