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
Received on Tue Dec 26 2017 - 21:30:02 PST
