Re: [AMBER] Can tLeap read SCNB and SCEE vales from frcmod file ? from Bill Ross on 2017-12-27 (Amber Archive Dec 2017)

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Wed, 27 Dec 2017 00:44:40 -0800

I haven't grasped what's going on in detail, but as far as I remember
from the 2-4 years I spent getting the original leap ready for
production ~20 years ago, the retired Gibbs program was the only way of
calculating free energies at the time, and the perturbation setup using
dummy atoms was targeted at it.

Bill

On 12/27/17 12:36 AM, Lachele Foley 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
>
> 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.
>
>
> 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
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>>>
>> _______________________________________________
>> AMBER mailing list
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>>
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Received on Wed Dec 27 2017 - 01:00:04 PST