Drug Design Update: Merk Molecular Force Field

Today we are releasing a new way to wiggle small molecules, the Merk Molecular Force Field (MMFF). This wiggle action uses a different scoring scheme (MMFF) than the current wiggle button. In the current implementation of wiggle, it is possible for the small molecule to “fold” in on itself. With MMFF, this shouldn’t be a problem. MMFF is also very good at optimizing hydrogen bonds and the torsional space of the small molecule. There are some optimization problems that need to be worked out with MMFF (as you can see from the videos), but for now, give it a try and let us know what you think! It should be noted that this is only available through the selection interface, for now.

Here are some comparison videos.
Small molecule with MMFF
Small molecule with Wiggle

In addition to the new wiggle of molecules, there are numerous bug fixes in this release. These include fixes for:

1) When switching menus, custom geometry does not disappear. (changing from design to pulling the molecule around)
2) Game freezes when rotamers are generated
3) Too much output in logs
4) When loop building around the ligand, game crashes
5) Replacing atoms crashes - a lot
6) Selection interface quirks

Enjoy, and please post all your bugs in feedback and suggestions and science questions right here in the thread.

( Posted by  free_radical 83 1754  |  Tue, 05/03/2016 - 19:06  |  10 comments )
0
bertro's picture
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Thanks, will give it a try

Thanks, will give it a try

bertro's picture
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Groups: Beta Folders
I am getting: Error during

I am getting: Error during initialization: Your database appears to be corrupted message at start of the client.

==>>log.txt extract

buildid: 20160503-de9a41d9eb-win_x86-experimental
about to create view_options_button_
Duplicate hotkey Shift+L (Show outlines, )
setting side chain mode to: 2 Show All (Slow)
Playing: sounds/organic_01/splashscreen.ogg
Converting any old-style quicksaves and autosaves...
Deleting any old temporary autosaves and quicksaves...
file: 'alignment/BLOSUM62' '8a453c755490e68a71be132741c00c88' != '2d84d18b63e63295f32873a50bea1c26'
Error during initialization:
Your database appears to be corrupted.
Please try reinstalling the application.

bertro's picture
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Groups: Beta Folders
I force a database

I force a database re-download from foldit and I get the same error again.

Also got this in ==>>debug.txt after the first time:

version: 1
{
"build_id" : "20160503-de9a41d9eb-win_x86-experimental"
"crash_id" : "bcf89e18-fc78-4e59-9e5f-8d3610366b7d"
"current_actions" : ""
"current_tool" : ""
"file" : "core/chemical/AtomTypeSet.cc:180"
"machine_id" : "09edfe6b-95dc-4576-888d-aeeae5d74622"
"macro_id" : "-1"
"message" : "Unable to open atomset file: cmp-database-e8c0958c2af768c33992a017b80451ce\\database\\chemical/atom_type_sets/fa_standard//atom_properties.txt"
"player_id" : "0"
"puzzle_id" : "0"
"puzzle_running_time" : "1034011"
"running_time" : "1.03401e+06"
"timestamp" : "1462318027"
}
verify: a74c684c00c38e6979983967cce2a1ec

Susume's picture
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Joined: 10/02/2011
same database error

I just updated my main install to experimental, and I get the same error: "Your database appears to be corrupted"

I did not get a debug.txt.
End of log.txt:

buildid: 20160503-de9a41d9eb-win_x86-experimental
about to create view_options_button_
Duplicate hotkey Shift+L (Show outlines, )
setting side chain mode to: 2 Show All (Slow)
Playing: sounds/organic_01/splashscreen.ogg
Converting any old-style quicksaves and autosaves...
file: 'alignment/BLOSUM62' '8a453c755490e68a71be132741c00c88' != '2d84d18b63e63295f32873a50bea1c26'
Error during initialization:
Your database appears to be corrupted.
Please try reinstalling the application.
exiting...
closing boinc...
Sending SOPs:

done.

Joined: 01/12/2015
Groups: None
Database Error

I just updated the binary. This should be fixed now. As far as I am aware, it should have only affected Windows users. Sorry about that!

You might have to start from scratch to fix this error...I am not sure.

bertro's picture
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Groups: Beta Folders
Thanks, it works!

Thanks, it works!

bertro's picture
User offline. Last seen 10 hours 13 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Crash on starting a shake

Crash on starting a shake (after a successful wiggle):

==>>log.txt

args passed:
'F:\FolditNEW\Main C\Foldit\Foldit.exe'
starting the init thread!..
boinc base url: https://fold.it
checking updates...
binary
local: 'd404eb36a9315608c9c8d15578ad595f'
remote: 'd404eb36a9315608c9c8d15578ad595f'
database
local: 'e8c0958c2af768c33992a017b80451ce'
remote: 'e8c0958c2af768c33992a017b80451ce'
resources
local: '614f6d95ff3682173087675b78c95ad6'
remote: '614f6d95ff3682173087675b78c95ad6'
cleaning up old components:
binary 00000000000000000000000000000000
binary b710150130080612504d41ac237f9633
Removing...
binary d404eb36a9315608c9c8d15578ad595f
database e8c0958c2af768c33992a017b80451ce
resources 00000000000000000000000000000000
resources 614f6d95ff3682173087675b78c95ad6
CRASH: 0
SoundTheme::load: cmp-resources-614f6d95ff3682173087675b78c95ad6\resources\sounds/organic_01
loading: cmp-resources-614f6d95ff3682173087675b78c95ad6\resources\sounds/organic_01/rotamer_land_00.ogg
loading: cmp-resources-614f6d95ff3682173087675b78c95ad6\resources\sounds/organic_01/rotamer_land_01.ogg
loading: cmp-resources-614f6d95ff3682173087675b78c95ad6\resources\sounds/organic_01/rotamer_land_02.ogg
loading: cmp-resources-614f6d95ff3682173087675b78c95ad6\resources\sounds/organic_01/rotamer_land_03.ogg
loading: cmp-resources-614f6d95ff3682173087675b78c95ad6\resources\sounds/organic_01/rotamer_land_04.ogg
loading: cmp-resources-614f6d95ff3682173087675b78c95ad6\resources\sounds/organic_01/rotamer_land_05.ogg
SVM classifier successfully loaded
Feature list successfully loaded
Valid classifier feature list
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 21
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LEU:CtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue THR:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue LYS:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASN:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 13
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ARG:CtermProteinFull 12
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 12
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASN:CtermProteinFull 12
buildid: 20160503-de9a41d9eb-win_x86-experimental
about to create view_options_button_
Duplicate hotkey Shift+L (Show outlines, )
setting side chain mode to: 2 Show All (Slow)
Playing: sounds/organic_01/splashscreen.ogg
Converting any old-style quicksaves and autosaves...
Deleting any old temporary autosaves and quicksaves...
Reading in vall_torsions file: cmp-database-e8c0958c2af768c33992a017b80451ce\database\sampling/rna/1jj2.torsions
Lines read from vall_torsions file: 2754
Sending SOPs:

Sending SOPs:

About to show the puzzle screen...
Trying to get the puzzle list...
Loading cache...
Parsing puzzle URL...
Parsing contests...
Parsing macros...
Saving the cache...
Parsing level completion...
Sending SOPs:

Initting the list...
Got the puzzles...
Sending SOPs:

Finished show_puzzle_screen...
has key .params
has key .2.params
has key .opdb
has key .opuzzle_setup
starting score : -99.6786
puzzle loaded
Autosave puzzles/0002002355/0000253386/default/autosave.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-best.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-recentbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-creditbest.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave3.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave4.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave5.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave6.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave7.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave8.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave9.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave10.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave11.ir_solution loaded.
Quicksave puzzles/0002002355/0000253386/default/quicksave12.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-best.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-recentbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-creditbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-best.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-recentbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/default/autosave-creditbest.ir_solution loaded.
GROUP CHAT CHANNEL: BetaFolders
clear density...
ScorePanel new session
BOINC says connect to: 128.95.1.227:6665
Using nick: bertro
Ended Initialization of NoviceGame
SRVR_THRD getting notifications...
Entering IRC::run
Sending SOPs:

IRC::run error, code = 5, desc = Remote connection closed
Exiting IRC::run
setting side chain mode to: 0 Don't Show (Fast)
Current Track: DHFR1
Autosave puzzles/0002002355/0000253386/DHFR1/autosave.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-best.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-recentbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-creditbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-best.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-recentbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-creditbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-best.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-recentbest.ir_solution loaded.
Autosave puzzles/0002002355/0000253386/DHFR1/autosave-creditbest.ir_solution loaded.
GROUP CHAT CHANNEL: BetaFolders
clear density...
ScorePanel new session
Sending SOPs:

Entering IRC::run
IRC::run error, code = 5, desc = Remote connection closed
Exiting IRC::run
***** STARTING THREAD ActionGlobalMinimize
delta_score: 401.272
Playing sound: 6
***** ENDING THREAD ActionGlobalMinimize
***** STARTING THREAD ActionRepack
delta_score: 0
Playing sound: 4

UNHANDLED EXCEPTION
1: alIsAuxiliaryEffectSlot +13459912 bytes (no line)
2: library_main +3334136 bytes (no line)
3: library_main +5054149 bytes (no line)
4: library_main +3726469 bytes (no line)
5: library_main +5198376 bytes (no line)
6: library_main +3702555 bytes (no line)
7: library_main +3243840 bytes (no line)
8: library_main +3938781 bytes (no line)
9: library_main +4949528 bytes (no line)
10: library_main +3518460 bytes (no line)
11: library_main +4785438 bytes (no line)
12: library_main +2973806 bytes (no line)
13: library_main +21918 bytes (no line)
14: library_main +21 bytes (no line)
15: no symbol (no line)
16: no symbol (no line)
17: no symbol (no line)
18: BaseThreadInitThunk +36 bytes (no line)
19: RtlUnicodeStringToInteger +595 bytes (no line)
20: RtlUnicodeStringToInteger +542 bytes (no line)

Joined: 01/12/2015
Groups: None
Did you edit the small

Did you edit the small molecule any before running the wiggle/shake. I noticed last night that the original ligand in the binding pocket may have some issues with it (not sure why). Your log doesnt show much that I can work with. I will try to reproduce it.

Joined: 01/12/2015
Groups: None
I can reproduce the error if

I can reproduce the error if I dont edit the ligand. What a weird bug. I will investigate!

Joined: 01/12/2015
Groups: None
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https://discord.gg/0zRrgd68uK1uDazx

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons