Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? from Lachele Foley on 2017-12-28 (Amber Archive Dec 2017)

From: Lachele Foley <lf.list.gmail.com>
Date: Fri, 29 Dec 2017 01:30:44 -0500

Some of the parameters we use come from other chemical types (like amino
acids). If those folks did a good job making parameters, we use them, in
the way they intended.

On Thu, Dec 28, 2017 at 3:49 AM, mish <smncbr.gmail.com> wrote:

> This is interesting. I always had this impression that SCEE=SCEE=1 is
> used invariably in GLYCAM. Ligand (sialic acid) has N-acetyl group so
> 1.2/2.0 in parm7 is actually for those two dihedrals (I checked it using
> without dummy atom). Many thanks for figuring it out.
>
> Sincerely,
> Mish
>
> On Thu, Dec 28, 2017 at 3:46 PM, Lachele Foley <lf.list.gmail.com> wrote:
>
> > Ok... yeah, sorry. I do know this...
> >
> > That's because two or more of the atom types are exactly the same as far
> as
> > the parameter list is concerned - so the list of types that are actually
> > different might be smaller than the list of names. It's a way to save
> > memory.
> >
> > So.... I'm pretty sure the scee and scnb values you want are being
> > applied. That became obvious when I gave them each separate SCEE and
> SCNB
> > values and they all showed up in the parm file. The 1.2 and 2.0 are
> almost
> > certainly from our parm file. For example:
> >
> > $ grep SCEE=1.2 /path/to/dat/leap/parm/GLYCAM_06j.dat
> > H -Ng-C -H1 1 -2.50 0.0 2. SCEE=1.2
> > SCNB=2.0 Parm94 - Corrected to remove phase shift
> > H -Ng-C -O 1 2.50 180.0 -2. SCEE=1.2
> > SCNB=2.0 Copy of Parm99 JCC,7,(1986),230 J.C.cistrans-NMA DE
> > 1 2.00 0.0 1. SCEE=1.2
> > SCNB=2.0
> >
> > These are present because they are amino-acid-like terms.
> >
> > The parameter-topology file is a complex thing... Decoding the info can
> be
> > tough. By the way, there are some pretty advanced parm-file utilities in
> > AMBER now. You can interrogate one pretty well with them. They would
> > probably tell you what values are being applied to what set of atoms.
> >
> > I'm still not optimistic about what you're trying to do. But, I wish you
> > luck.
> >
> >
> > On Wed, Dec 27, 2017 at 7:23 AM, mish <smncbr.gmail.com> wrote:
> >
> > > Many thanks for the debugging the problem. However, I guess this
> behavior
> > > need a check. For example the atom_type and Index issue below:
> > >
> > > On Wed, Dec 27, 2017 at 5:36 PM, Lachele Foley <lf.list.gmail.com>
> > wrote:
> > >
> > > > The main problem is that you can't really use dummy atoms that way in
> > > > AMBER. There might be other issues, too. Jason Swails or Dan Roe
> > might
> > > be
> > > > able to help you if you feel you must do it the way you're doing it.
> > > But,
> > > > that might not be possible at all.
> > > >
> > > > Currently, AMBER does TI (or other atom-changing methods) using two
> > > > topology files (or maybe one combined one for pmemd). Years ago, you
> > > would
> > > > use explicit dummy atoms. You had to specify them separately in leap
> > as
> > > > perturbed atoms or such. It's been about a decade since I did it
> that
> > > way,
> > > > and I only remember it a little. I don't recall if you would be able
> > to
> > > > use the mol2 file as-is, but you'll have to resurrect ancient leap
> > > > perturbation commands that aren't used anymore (so if they don't
> work,
> > > > you're kindof on your own if you want that fixed).
> > > >
> > > > Whatever is the proper way to do what you're trying to do, at present
> > > leap
> > > > has no clue how to do what you're asking for.
> > > >
> > > > A big symptom of the problem is in the file's handling of the number
> of
> > > > atom types. The parm file happily lists all 15 types (I count 15) in
> > > > the AMBER_ATOM_TYPE section. But, in the POINTERS section, the file
> > > thinks
> > > > there are only 11 types. And, if you look in the ATOM_TYPE_INDEX,
> you
> > > will
> > > > find that there is no number larger than 11. I don't know why it
> stops
> > > at
> > > > 11. The reason for that isn't entirely obvious to me.
> > >
> > > However, when I make your entries say this:
> > > >
> > > > DIHEDRAL
> > > > Ng-C -Cg-zz 1 0.25 0.0 3. SCEE=9.9
> > > > SCNB=9.9 Dimethylammonium
> > > > C -Cg-zz-du 1 0.25 0.0 3. SCEE=8.8
> > > > SCNB=8.8 N,N-Dimethyl amine
> > > > Hc-Cg-zz-du 1 0.25 0.0 3. SCEE=7.7
> > > > SCNB=7.7 N,N-Dimethyl amine
> > > > zz-Cg-C -O 1 0.20 0.0 3. SCEE=6.6
> > > > SCNB=6.6 Methyl propanoate
> > > >
> > > > (note 9.9, 8.8, 7.7 and 6.6)...
> > > >
> > > > All four of them are, indeed, printed in the list (below). But, I
> > don't
> > > > know how those are even being referenced if those atoms aren't even
> > being
> > > > assigned a type index. I suspect you would get really bad results or
> > > even
> > > > a seg fault if you tried to run a simulation with this file.
> > > >
> > > > %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 8.80000000E+00
> > > > 7.70000000E+00
> > > > 6.60000000E+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 8.80000000E+00
> > > > 7.70000000E+00
> > > > 6.60000000E+00 0.00000000E+00 0.00000000E+00
> > > >
> > > > So.... you can't really do what you're trying to do. And, leap is
> > > getting
> > > > mightily confused while trying to help you out despite that.
> > > >
> > > > The use of 1.2 and 2.0 is likely a result of the confusion. Without
> a
> > > code
> > > > audit, I can barely begin to guess what leap is really doing.
> > > >
> > > > Here is the atom type section. Note that there are 15 unique types.
> > > >
> > > > %FLAG AMBER_ATOM_TYPE
> > > > %FORMAT(20a4)
> > > > H1 Cg H1 H1 Os Cy C O2 O2 Cg Hc Hc Cg H1 Cg H1 Cg
> H1
> > > Cg
> > > > H1
> > > > Cg H1 Cg H1 H1 Oh Ho Oh Ho Oh Ho Oy Ng H C Cg Hc
> Hc
> > > zz
> > > > O
> > > > Oh Ho du
> > > >
> > > > Here is the atom type index section, and notice that they only go up
> to
> > > 11
> > > > (insert Spinal Tap humor as desired at this point).
> > > >
> > > > %FLAG ATOM_TYPE_INDEX
> > > > %FORMAT(10I8)
> > > > 1 2 1 1 3 2 4 5
> > 5
> > > > 2
> > > > 6 6 2 1 2 1 2 1
> > 2
> > > > 1
> > > > 2 1 2 1 1 7 8 7
> > 8
> > > > 7
> > > > 8 3 9 10 4 2 6 6
> > 11
> > > > 5
> > > > 7 8 11
> > > >
> > > >
> > > It behaves similaily if I use glycam06 and write a parm7 file for
> > > > methylated sialic acid {OME 0SA}. I loaded a pdb file not created it
> > rom
> > > > sequence. tleap writes 13 AMBER_ATOM_TYPE (H1 Cg Os Cy C O2 Hc
> > > > Oh Ho Oy Ng H O) and pointer stops at 10 (ATOM_TYPE_INDEX) in
> > parm7.
> > > > This seems to be consistent as I just had an additional dummy atom in
> > > this
> > > >
> > >
> > >
> > > %FLAG AMBER_ATOM_TYPE
> > >
> > > %FORMAT(20a4)
> > >
> > > H1 Cg H1 H1 Os Cy C O2 O2 Cg Hc Hc Cg H1 Cg H1 Cg H1
> > Cg
> > > H1
> > >
> > > Cg H1 Cg H1 H1 Oh Ho Oh Ho Oh Ho Oy Ng H C Cg Hc Hc
> > Hc
> > > O
> > >
> > > Oh Ho
> > >
> > >
> > >
> > > %FLAG ATOM_TYPE_INDEX
> > >
> > > %FORMAT(10I8)
> > >
> > > 1 2 1 1 3 2 4 5
> 5
> > > 2
> > >
> > > 6 6 2 1 2 1 2 1
> 2
> > > 1
> > >
> > > 2 1 2 1 1 7 8 7
> 8
> > > 7
> > >
> > > 8 3 9 10 4 2 6 6
> 6
> > > 5
> > >
> > > 7 8
> > >
> > >
> > >
> > > > So, you might need to talk to the makers of the other program you
> want
> > to
> > > > use. Or troll old mailing list threads and old versions of the
> manual
> > > > (AMBER 8 or so should be right) to figure out how to do it that way.
> > > See a
> > > > current version of the manual for how to do TI currently. I haven't
> > done
> > > > it recently, so I don't know the details. But, if you write with
> > > questions
> > > > about setting up files for Ti, you should get help.
> > > >
> > > > That's the best I've got for now. Sorry I couldn't help more.
> > > >
> > >
> > >
> > > > I am aware of setting up TI in pmemed/sander. As of now I am writing
> > some
> > > > patches that allow using using GLYCAM in another tool siremol. It
> > requres
> > > > amber format parm7 file togather with a file that contains charges,
> > vdw,
> > > > angle, dihedrals etc values which are morphed betwen two states. This
> > is
> > > > why I need to start with dummy atoms.
> > > >
> > >
> > > >
> > > On Wed, Dec 27, 2017 at 12:09 AM, mish <smncbr.gmail.com> wrote:
> > > >
> > > > > 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
> > > > > > >>>>>>>>>> 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
> > > > > > >>>>>> _______________________________________________
> > > > > > >>>>>> 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
> > > > > > >>>> _______________________________________________
> > > > > > >>>> 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
> > > > > > >> _______________________________________________
> > > > > > >> 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
> > > > _______________________________________________
> > > > 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
> > _______________________________________________
> > 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 Thu Dec 28 2017 - 23:00:03 PST