openforcefield amber-ff-porting issues

openforcefield / amber-ff-porting

Scratch space for porting amber FFs into SMIRNOFF format

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issues

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Restricted benchmark to ARG/HIS to find a problem

#46 pbuslaev closed 9 months ago
0
Added additional output for testing

#45 pbuslaev closed 9 months ago
0
Add CYM

#44 j-wags closed 8 months ago
52
Removing openeye dependency and allowing porting patches

#43 pbuslaev opened 9 months ago
3
Include CYM parameters in ff14sb port

#42 pbuslaev closed 9 months ago
4
Add CYM parameters

#41 j-wags closed 7 months ago
2
[DNM]: Conversion to version 0.0.3

#40 mattwthompson closed 2 years ago
1
Remove aromaticity(and probably formal charges and bond orders) from TRP sidechain

#39 j-wags closed 2 years ago
1
Remove stereo marks from protein FF

#38 j-wags closed 2 years ago
0
Make a release with `fractional_bondorder_method = "AM1-Wiberg"`

#37 mattwthompson closed 2 years ago
0
Failure with SMIRNOFF-style impropers

#36 mattwthompson closed 2 years ago
6
Update for OpenFF Toolkit namespace migration

#35 mattwthompson closed 2 years ago
2
[WIP] Parameter deduplication initial work

#34 connordavel closed 2 years ago
1
Protein fragments for testing OFF result

#33 dscerutti opened 3 years ago
1
Remove unused files and rename existing ones for clarity

#32 j-wags closed 3 years ago
0
Capture NTerminal backbone parameters and exclude malformed structures

#31 j-wags closed 3 years ago
0
Control for HIS Resonance

#30 j-wags closed 3 years ago
0
Write ARG sidechain guanidinium SMARTS using wildcard bonds to match all resonance forms

#29 j-wags closed 3 years ago
0
Malformed tripeptide mol2s

#28 j-wags opened 3 years ago
1
LYN_ARG chemical perception fails

#27 j-wags closed 3 years ago
2
GLN_HIP chemical perception fails

#26 j-wags closed 3 years ago
5
Proline energies

#25 j-wags opened 3 years ago
1
NTerm LEU energy discrepancies

#24 j-wags opened 3 years ago
1
ASN/GLN energy discrepancies

#23 j-wags closed 3 years ago
4
[WIP] Add backbone parameters

#22 j-wags closed 3 years ago
2
Fix #20 by ensuring CYX appears before CYS in each section

#21 j-wags closed 3 years ago
1
CYS library charges are being mis-applied

#20 j-wags closed 3 years ago
0
Backbone parameters

#19 j-wags closed 3 years ago
0
Remaining improper energy differences

#18 j-wags closed 3 years ago
6
Try matching exact improper order

#17 j-wags closed 3 years ago
1
Fix improper energies

#16 j-wags closed 3 years ago
9
NTerm GLU torsion energies are bad

#15 j-wags closed 3 years ago
4
Don't add redundant dihedral terms when they are seen multiple times in one structure

#14 j-wags closed 3 years ago
0
CYX dihedral energies are wrong

#13 j-wags closed 3 years ago
4
Problem with histidine chemical perception

#12 j-wags opened 3 years ago
6
divide impropers by 3, make test_parameterize loop over all residues

#11 j-wags closed 3 years ago
0
Workaround for #2 by overriding bond orders in carboxylates

#10 j-wags closed 4 years ago
1
C-terminal PRO.mol2 is created with incorrect partial charges

#9 j-wags opened 4 years ago
1
Make sure potentially promiscuous capping group parameters are at top of parameter hierarchy

#8 j-wags closed 3 years ago
1
Prototype of turning OpenMM system into an AMBER prmtop

#7 j-wags opened 4 years ago
0
Make prototype of using OpenMM to compute energies from prmtop + coordinates

#6 j-wags closed 3 years ago
1
Validation efforts for force field conversion

#5 dscerutti opened 4 years ago
1
Proline SMARTS can't be processed

#4 j-wags closed 4 years ago
1
Deduplicate redundant parameters caused by equivalent hydrogens

#3 j-wags closed 2 years ago
1
C termini are percieved to have a -3 charge

#2 j-wags opened 4 years ago
8
Residue truncation makes SMARTS too strict

#1 j-wags closed 4 years ago
0