Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ?

From: mish <smncbr.gmail.com>
Date: Wed, 27 Dec 2017 09:27:32 +0900

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
> >>> _______________________________________________
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> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
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> >>
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Received on Tue Dec 26 2017 - 16:30:03 PST
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