Update smirnoff99Frosst to remove generics in DrugBank #232

bannanc · 2017-03-16T21:24:25Z

This pull request will include parameters needed to match most of the chemistry in the larger set DrugBank. It still is no metals and molecules with <= 200 heavy atoms.

In this message I will list all of the changes I've made with links to issues where they have been discussed.

Parm99 or Parm@Frosst

Bonds

Remove neutral requirement in the bonds to hypervalent sulfur ( [#16X3+0,#16X4]) (issue Find missing parameters in smirff99Frosst for DrugBank #216 )
- The relevant atom type from parm@Frosst is applied to at least neutrally and negatively charged trivalent sulfurs. So the plan was to remove the +0
- There is a special case for sulfur carbon bonds. bonds for divalent (not hypervalent) sulfur come before these hypervalent bonds. In that section there is a S-C bond for [#16X2,#16X1-1,#16X3+1:1] sulfurs. We do not want the hypervalent sulfur bond to over ride these S-C bonds. So the SMIRKS pattern for hypervalent sulfur singly bound to carbon was set as [#16X4,#16X3!+1:1]-[#6]
Add C=S bond from parm@frosst (issue Find missing parameters in smirff99Frosst for DrugBank #216 )
removed X1 requirement for nitrogen in nitrile (issue Find missing parameters in smirff99Frosst for DrugBank #216 )
- the atomtype in parm99/parm@frosst matches #7X1 and #7X2&(*#*) so it is the triple bond that is important.
removed X4 requirement for the most generic S-C bond. (issue Find missing parameters in smirff99Frosst for DrugBank #216 )
C-[halogen] bonds to cover all carbons (smirnoff99Frosst issue#27)
remove X2 requirement from sulfur in S-H bond (smirnoff99Frosst issue#31)
Made some bonds more generic to address odd corner cases (smirnoff99Frosst issue#34)
- Remove X3 requirements for most generic N-N to cover N+1 cases
- Change [#6X4:1]-[#8X2:2] to [#6:1]-[#8:2] to cover corner cases
- Remove X2 on carbon in nitrile bonds to address charged corner cases
Changed order of carbonyl bonds to properly type carbonyl groups (smirnoff99Frosst issue#38)
Changed the first carbonyl group to be more general for groups of the type X=C=O as discussed in issue smirnoff99Frosst issue#37

Angles

added slightly more generic #7X2 angle for linear case (R-C#N+1-R)
made the X-N-O angles in nitro groups generic enough for X to be carbon, oxygen, or nitrogen (smirnoff99Frosst issue#36)
Updated most generic divalent sulfur to accomodate aromatic cases (smirnoff99Frosst issue#34)
- waiting approval

Torsions

Updated aromatic nitrogen torsion to cover all generic -N:C- cases (smirnoff99Frosst issue#39)
- waiting for approval
Remove neutral requirement in the bonds to hypervalent sulfur ( [#16X3+0,#16X4]) (smirnoff99Frosst issue#40 )
- The relevant atom type in parm@Frosst is SO which is for all #16X3, but in smirnoff there are some higher priority cases with #16X3+1 we wanted to remove the neutral requirement without overwriting those.
- waiting approval
Added torsion for nitro group-tetrahedral carbon based on parm@Frosst and GAFF2 (smirnoff99Frosst issue#42)
- waiting approval

Estimates from GAFF2

Bonds

S-P bond (smirnoff99Frosst issue#20)
H-P bond (smirnoff99Frosst issue#21)
N-halogen bonds (smirnoff99Frosst issue#24)
P-halogen bonds (smirnoff99Frosst issue#26)
S-halogen bonds (smirnoff99Frosst issue#33)

Angles

Torsions

-O-O- torsion (smirnoff99Frosst issue#23)
-S=,:-C- torsion (smirnoff99Frosst issue#41)
- waiting approval
-P-N- torsions (smirnoff99Frosst issue#32)
- waiting approval

davidlmobley · 2017-03-16T23:58:06Z

@bannanc - I'm going to suggest edits to your summary above since this is our record for posterity. Here are a couple of things which are unclear to me:

Our original plan was to remove the +0, however, there were bonds specified above for the case of #16+1 to carbon so to avoid overwriting those, the carbon bond was changed to [#16X4,#16X3!+1]

What's "specified above" mean? I'm guessing you mean "above this in the force field file"? Also, the reference of "the carbon bond" could be more clear -- THIS carbon bond? Or the one above? (Again, presumably you mean the former, but it's easier if it's just clear when you write it the first time so one doesn't have to stop and think about it.)

… updatesmirff pull changes in master

Merging Master

I fixed some of the comments

bannanc · 2017-04-05T02:00:40Z

@davidlmobley
Assuming you approve the newest round of changes. This now types all the filtered drugbank molecules, that have tripos mol2 files.

Note - there are a few corner cases we don't quite catch in the full DrugBank set.

My next plan is to close all the issues this pull request addresses and then open a single (LONG) issue with chemistry that we think needs to be explored further. That will include anything we got from GAFF2, things we don't cover now (i.e. boron/silicon), and anything where we made things fairly generic to cover our bases. This will serve as a source of molecules/functional groups for the undergrad in our group during the summer.

bannanc · 2017-04-05T02:02:40Z

For reference:

Charged Tripos mol2 files of filtered drugBank

GAFF2 typed molecules for filtered DrugBank

davidlmobley · 2017-04-05T04:32:35Z

@bannanc :

My next plan is to close all the issues this pull request addresses and then open a single (LONG) issue with chemistry that we think needs to be explored further. That will include anything we got from GAFF2, things we don't cover now (i.e. boron/silicon), and anything where we made things fairly generic to cover our bases. This will serve as a source of molecules/functional groups for the undergrad in our group during the summer.

This plan sounds excellent.

Reviewing FF changes in a cursory way (since I already reviewed all the individual issues in detail) now.

davidlmobley · 2017-04-05T04:33:41Z

And, once merged, you will also migrate these changes to github.com/open-forcefield-group/openforcefield and github.com/open-forcefield-group/smirnoff99frosst, @bannanc ? (We're working towards removing smirnoff from smarty).

davidlmobley · 2017-04-05T04:34:17Z

utilities/convert_frosst/smirffishFrcmod.parm99Frosst.txt

-# Updated: Many times during Fall 2016 - Winter 2017, most recently Fri. March 3, 2017
+# Date: only last line in this section is used, all others in list will be ignored. 
+DATE
+# Updated: Many times during Fall 2016 - Winter 2017, small change with eithers Fri. March 3, 2017


"ethers" not "eithers". :)

davidlmobley

LGTM, @bannanc !

bannanc · 2017-04-05T06:03:41Z

@davidlmobley if you're ok with what I did with the aromatic nitrogen torsion then I think this is good to know with the knowledge that we'll probably have another one in the not too distant future.

davidlmobley · 2017-04-05T15:53:17Z

@bannanc - tests are failing because the tests load smirff99Frosst.ffxml but you renamed to smirnoff99Frosst.ffxml. Can you fix?

Failure: ValueError (Sorry! /home/travis/miniconda/envs/test/lib/python2.7/site-packages/smarty/data/forcefield/smirff99Frosst.ffxml does not exist. If you just added it, you'll have to re-install) ... ERROR

davidlmobley · 2017-04-05T15:53:32Z

(It's OK with me if you go ahead and merge once tests pass, @bannanc !)

I didn't change anything in the XML format because I didn't want to break it, but presumably we'll need to update that too

davidlmobley · 2017-04-05T21:51:05Z

@bannanc - looks like py27 and py35 passed on your last commit, but py34 is failing. Checking.

bannanc · 2017-04-05T21:52:35Z

The most recent run failed on python3 and not python2, but the failure said it didn't get 100% on the AlkEthOH answers... I don't think we changed anything in the AlkEthOH parameters on this set. I'll see if the same problem repeats on this test

davidlmobley · 2017-04-05T21:52:46Z

Well, that's really weird... Py34 test failed with something you haven't touched in here:

FAIL: Test score is 100% if correct VdW, Bond, Angles, or Torsions
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/miniconda/envs/test/lib/python3.4/site-packages/smarty/tests/test_smirky_sampler.py", line 53, in test_correct_fragments
    self.assertAlmostEqual(fracfound, 1.0, msg = "Not finding 100%% of AlkEthOH when starting from correct %s SMIRKS." % typetag)
AssertionError: 0.9962640099626401 != 1.0 within 7 places : Not finding 100% of AlkEthOH when starting from correct VdW SMIRKS.

I think the SMIRKY test may have accepted a very rare move which resulted in losing some coverage of the AlkEthOH set, perhaps, just in this one case? Looks like it should be good to merge when you are ready, @bannanc .

bannanc · 2017-04-05T22:06:17Z

~~I'm going to make the number of steps on the 100% test smaller to avoid that happening in the future.~~

Nevermind, it already has 2 steps and temperature = 0.0 it shouldn't ever accept moves that decrease the score... I don't know what caused the failed test assuming this one passes I'll merge it.

bannanc changed the title ~~Update smirff99Frosst to remove generics in DrugBank~~ [WIP] Update smirff99Frosst to remove generics in DrugBank Mar 16, 2017

bannanc mentioned this pull request Mar 16, 2017

Convert_frcmod.py should take dates and authors from the smirffishFrcmod file #233

Closed

bannanc and others added 9 commits March 28, 2017 15:12

Merge branch 'master' of github.com:open-forcefield-group/smarty into…

6174aeb

… updatesmirff pull changes in master

update S-H bond

e202107

add S-halogen bonds

22bebe1

more generic C-O, N-N, and C#N

ff5476b

update nitro group to also cover oxygen and nitrogen

be337bf

update carbonyl and carboxylate groups

c9bd98d

Angles with nitro groups

6c368f4

parameter notebook

c73ec52

Merge pull request #246 from open-forcefield-group/master

a0c3490

Merging Master

bannanc mentioned this pull request Apr 4, 2017

Confusing trivalent sulfur that shouldn't get a generic but does openforcefield/smirnoff99Frosst#40

Closed

added missing torsions and a few angles, maybe

309b524

bannanc changed the title ~~[WIP] Update smirff99Frosst to remove generics in DrugBank~~ [WIP] Update smirffno99Frosst to remove generics in DrugBank Apr 5, 2017

update comments

5e91bfd

I fixed some of the comments

davidlmobley reviewed Apr 5, 2017

View reviewed changes

davidlmobley approved these changes Apr 5, 2017

View reviewed changes

ether typo

6ab5680

bannanc changed the title ~~[WIP] Update smirffno99Frosst to remove generics in DrugBank~~ Update smirffno99Frosst to remove generics in DrugBank Apr 5, 2017

rename smirff in smarty/data/forcefield/smirff to smirnoff

831662b

bannanc mentioned this pull request Apr 5, 2017

rename to smirnoff and add changes in smarty pull request openforcefield/smirnoff99Frosst#43

Merged

update with smirnoff names

6e8740e

bannanc added 3 commits April 5, 2017 12:53

smirff rename

dff664c

smirnoff renaming

fbd8628

smirff renaming

22f163d

I didn't change anything in the XML format because I didn't want to break it, but presumably we'll need to update that too

davidlmobley changed the title ~~Update smirffno99Frosst to remove generics in DrugBank~~ Update smirnoff99Frosst to remove generics in DrugBank Apr 5, 2017

Merge branch 'master' into updatesmirff

fccbf18

bannanc merged commit 4541186 into master Apr 5, 2017

This was referenced Apr 5, 2017

Depicting molecules in python3 #245

Closed

Find missing parameters in smirff99Frosst for DrugBank #216

Closed

bannanc deleted the updatesmirff branch January 24, 2018 21:05

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Update smirnoff99Frosst to remove generics in DrugBank #232

Update smirnoff99Frosst to remove generics in DrugBank #232

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Update smirnoff99Frosst to remove generics in DrugBank #232

Update smirnoff99Frosst to remove generics in DrugBank #232

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bannanc commented Mar 16, 2017 • edited Loading

Parm99 or Parm@Frosst

Estimates from GAFF2

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