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

From: mish <smncbr.gmail.com>
Date: Wed, 27 Dec 2017 14:09:11 +0900

Oh, Sorry! Thank you.

On Wed, Dec 27, 2017 at 2:06 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:

> You misstyped an 'l' as an 'i' if the quoted email quotes the addr right.
>
> Bill
>
>
> On 12/26/17 8:56 PM, mish wrote:
> > 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
> >>>>>>>>>>> AMBER.ambermd.org
> >>>>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>>>>>
> >>>>>>>>>> _______________________________________________
> >>>>>>>>>> AMBER mailing list
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> >>>>>>>>>>
> >>>>>>>>> _______________________________________________
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> >>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> AMBER mailing list
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> >>>>>>>>
> >>>>>>> _______________________________________________
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> >>>>>>> AMBER.ambermd.org
> >>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>>
> >>>>>>
> >>>>>>
> >>>>>> --
> >>>>>> :-) Lachele
> >>>>>> Lachele Foley
> >>>>>> CCRC/UGA
> >>>>>> Athens, GA USA
> >>>>>> _______________________________________________
> >>>>>> AMBER mailing list
> >>>>>> AMBER.ambermd.org
> >>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>>>
> >>>>> _______________________________________________
> >>>>> AMBER mailing list
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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
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
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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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>
>
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Received on Tue Dec 26 2017 - 21:30:02 PST