`Toppar change log

All files in the toppar subdirectory that are included in the final
release (eg. files in toppar_jul16/toppar) will be maintained in the
Michigan GIT.  The procedure will allow for the files to be maintained
locally at UMB and then uploaded into the git repository prior to new
releases of CHARMM.Information on performing the process is in the
MacKerell lab wiki.  

http://mackerell.umaryland.edu/pmwiki/pmwiki.php?n=Main.CharmmGitRepositoryAtUMich

see 00git_information.txt for details of exact commands used to
upload files into the git repository.

1) Proteins

1a) Added residues for phosphorylated Tyr (TPA), Thr (TPO) and Ser (SEP) to
toppar_all36_prot_na_combined.str

1b) par_all36_prot.prm and par_all36m_prot.prmL following angle and dihedral
parameter for neutral termini added.  All parameters based on analogy

NH2  CT1  CT2A  67.700    110.00              ! From LSN NH2-CT2-CT2
NH2  CT1  CD    50.000    107.00              ! From ALA Dipep. NH1-CT2-C
NH2  CT2  CD    50.000    107.00              ! From ALA Dipep. NH1-CT2-C, Neutral Gly Nterminus

NH2  CT1  C    O        0.0000  1     0.00
NH2  CT2  C    N        0.0000  1     0.00   ! NNEU
NH2  CT1  CT2A HA2      0.2000  3     0.00 ! From X    CT1  CT2  X
H    NH2  CT1  CD       0.0000  1     0.00
H    NH2  CT2  CD       0.0000  1     0.00   ! Neutral Gly Nterminus
H    NH2  CT1  CT2A     0.1100  3     0.00   ! From LSN HC-NH2-CT2-CT2
CC   CT2A CT1  NH2      0.6800  1   180.00   ! From CC   CT2A CT1  NH1
CC   CT2A CT1  NH2      0.1000  2   180.00
CC   CT2A CT1  NH2      0.3800  3     0.00
CD   CT1  CT2A CC       1.6100  1   180.00   ! From C    CT1  CT2A CC
CD   CT1  CT2A CC       1.2900  2   180.00
CD   CT1  CT2A CC       0.5900  3   180.00

1c) top_all36_prot.prm: In PRES CNEU atom name HT2 changed to HT2B to
avoid conflict with PRES NNEU.

1d) Residues and patches for methylhistidine have been created for both
the neutral and charged states. The new terms have been added to
toppar_all36_prot_modify_res.str.

! Full residues that may be used when a full protein is being generate
  and the appropriate residues have been renamed as follows.

RESI HIC: neutral methylhistidine
RESI HICP: charged methylhistdine

! Patches to convert standard CHARMM histidine residues to
  methylhistidine. Its necessary to apply the correct patch to the
  appropriate parent residue.

PRES MHSE: convert HSE to methylhistidine
PRES MHSD: convert HSD to methylhistidine (methyl still NE2 atom)
PRES MHSP: converg HSP to protonated methylhistidine

see /raid/alex/param/toppar_jul18/new_prot/methylhistidine


2) Carbohydrates

2a) Added toppar_all36_carb_lignin.str into the stream/carb
subdirectory. These contain the Lignin parameters from Vermaas et al.
Test case added: test_all36_carb_lignin.inp

!references
!
!Vermaas et al., "Systematic parameterization of lignin for the CHARMM
!force field, " Green Chemistry 21: 109, 2019, DOI: 10.1039/c8gc03209b
!
!Vermaas et al., "Automated Transformation of Lignin Topologies into
!Atomic Structures with LigninBuilder," ACS Sustainable
!Chem. Eng. 7:3443, 2019, DOI: 10.1021/acssuschemeng.8b05665

2b) par_all36_carb.prm: Additional optimization of N-acetyl group
dihedral parameters.  Leads to improved treatment of N-acetyl
conformational sampling in GlcNAC, GalNAC and Neu5NAC.

2c) Miscellaneous parameters added by analogy.

OC302   CC3162  CC3161  NC2D1    0.20  3    0.0 ! par27 X CTL1 CTL1 X

3) Lipids

2a) TMA-aromatic group cation-pi interaction parameters 

toppar_all36_lipid_cationpi_wyf.str added to stream/lipid

!reference Khan, MacKerell, Jr., and Reuter, "Cation-π Interactions
!between Methylated Ammonium Groups and Tryptophan in the CHARMM36
!Additive Force Field," J. Chem. Theory Comput. 2019, 15, 1, 7-12,
!DOI: 10.1021/acs.jctc.8b00839

4) CGenFF: 2018-2019 changes to CGenFF to version 4.3

4a) New residues added
RESI NC2       1.000 ! dimethylammonium  fylin/kenno
RESI NC3       1.000 ! trimethylammonium  fylin/kenno
RESI NH4       1.000 ! ammonium fylin/kenno
RESI TEAZ      0.000 ! C1H2N4, 1H-tetrazole  pchat
RESI MTEA      0.000 ! C2H4N4, 5-Methyl-1H-tetrazole pchat
RESI ETEA      0.000 ! C3H6N4, 5-Ethyl-1H-tetrazole pchat
RESI 2OXT      0.000 ! 2-Oxetanone ozyo
RESI 3OXT      0.000 ! 3-Oxetanone ozyo
RESI BUTY      0.000 ! 1-butyne pchat
RESI PNTY      0.000 ! 1-pentyne pchat
RESI HXYN      0.000 ! 1-hexyne pchat
RESI HPTY      0.000 ! 1-heptyne pchat
RESI OCTY      0.000 ! 1-octyne pchat
RESI BEYN      0.000 ! But-1-ene-3-yne pchat
RESI PRF       1.000 ! (2-amino-4-oxo-1,7-dihydropyrrolo[2,3-d]pyrimidin-5-yl)methylazanium ; ashal

4b) NBFIX terms added for halogen-protein interations. Important for
halogenated ligand-protein interacions.  Analogous parameters added
for carbohydrates, lipids, and nucleic acids.

Lin, F.-Y. and MacKerell Jr., A.D., “Improved Modeling of Halogenated
Ligand-Protein Interactions using the Drude Polarizable and CHARMM
Additive Empirical Force Fields,” JCIM, 59: 215-218, 2019,
10.1021/acs.jcim.8b00616, PMC6349471

4c) Reorganization of both the topology	and parameter files to allow
for integration of the release files with those used to train the
CGenFF program.  This will facilitate training of the CGenFF program
in the future as well as assure that the release and CGenFF program
based parameter files are consistent.  This included a couple minor
changes in partial atomic changes.  This will make the charges in the
topology file consistent with those output by the CGenFF program.

Version 4.3 of top_all36_cgenff.rtf and par_all36_cgenff.prm is
synchronized with Version 2.3 of the CGenFF program.

4d) Improper atom order correction
RESI GUAN 
RESI MGUA
Minor charge changes in CH2 or CH3 groups
RESI GLYN
RESI MAMM
RESI EAMM
RESI METO
RESI ETO

5) Water-ion toppar file

5a) Calcium NBFixes added: 2019-8
CAL    CLA      -0.134164   3.727 ! from J. Phys. Chem. B 2018, 122, 1484−1494
CAL    O2L      -0.12       3.256 ! from J. Phys. Chem. B 2018, 122, 1484−1494
CAL    OC2DP    -0.12       3.256 ! from J. Phys. Chem. B 2018, 122, 1484−1494
CAL    OG2P1    -0.12       3.256 ! from J. Phys. Chem. B 2018, 122, 1484−1494
!
CAL    OCL      -0.12       3.232 ! Rong Shen and Benoit Roux, personal communication
CAL    OC       -0.12       3.232 ! Rong Shen and Benoit Roux, personal communication
CAL    OC2D2    -0.12       3.232 ! Rong Shen and Benoit Roux, personal communication
CAL    OG2D2    -0.12       3.232 ! Rong Shen and Benoit Roux, personal communication

5b) added hydrogen peroxide (h2o2) rtf and parameters

 see https://pubs.acs.org/doi/10.1021/acs.jctc.8b00246

6) Toppar test cases in test subdirectory updated: 2019_7

test case input file restructured to read all toppar files by each
test case as listed in ./toppar.str. This allows dependencies between
the various toppar files to be taken into account.  This leads to
issues with overlapping residues/patch names that required a few
renaming of residues and patches (see below). Those changed were on
residues/patches that are rarely used and therefore will not impact
the large majority of users.

One problem with this is that the test cases run significantly slower
due to the reading of all the toppar files by each job.

toppar_all36_na_modifications.str
change name of residue CYTP to CYPR
RESI CYPR         1.00  ! To Protonate C5-Me CYT at N3, edarian 2009-03, previously CYTP
                        !avoid clash with PRES CYTP in toppar_all36_na_rna_modified.str

toppar_all36_prot_na_combined.str
change name of patch THP2 to THPB
PRES THPB        -2.00  ! convert threonine to dianionic phosphothreonine
                        ! use in a patch statement, previously THP2

toppar_all36_prot_model.str
change name of residue from TP2 to TP2Z
RESI TP2Z        1.00 ! prolineamide, R. Dunbrack, previously TP2

toppar_all36_prot_pyridines.str
change name of residue from PYR1 to PYRE
RESI PYRE        0.00 ! pyridine, previously PYR1

toppar_all36_carb_lignin.str
change name of patch from AOG to AOG1
PRES AOG1 0.00 ! alpha to gamma ester linkage, formally AOG

7) Addition of UIUC ion NBFIX parameters in non_charmm/toppar_ions_nbfix_uiuc.str

toppar_ions_nbfix_uiuc.str: Contains a variety of NBFIX terms
optimized by Yoo and Aksimentiev, Univ of Illinois,
Urbana-Charmpaign. See the file for the approprate references.  As
these conflict with some of he defaul CHARMM36 additive NBFIX terms
they have not been included with the default toppar files. Note that
these are not tested.

8) Below is the list of Im lab changes and additions.

Done	1. toppar_water_ions.str: changes already in UMB file
		=95 NBFIX for Ca2+ ion
		=95 NBFIX for pyrophosphate (related to #9)

Done	2. toppar_all36_lipid_detergent.str: new lipid LPPG added to test case
		=95 Bug fix: charge for DDAOP
		=95 New lipids: STIG, SITO, LPPG, TSPC: only LPPG in the new toppar_all36_lipid_detergent.str

Done	3. toppar_all36_prot_d_aminoacids.str: also added to all36m version
		=95 Missing parameters for D-amino acids
			=95 CT1  NH1  C    CTD1     1.6000  1     0.00
			=95 CT1  NH1  C    CTD1     2.5000  2   180.00

Done	4. toppar_all36_carb_imlab.str: test case updated
		=95 Bug fix: 2ANA/2BNA patches for P. aeruginosa
		=95 Bug fix: IC table for 6TPEAP
		=95 Bug fix: IC table for DPHG / DPHGA
		=95 Bug fix: missing parameters for GPI
		=95 Update: 2ANSF / 2BNSF patches
		=95 New patch: FP17BT for BGALF 1->7 AHEP linkage: test case updated
                alex: patch name changes: sa24bb to sa24ab and SA25BA to SA25AA
                alex: patch name changes: SA28BT to SA28AT

Done	5. toppar_all36_lipid_model.str (was already changed)
		=95 Change residue name GLYP =97> GLPH

Done	6. top_all36_prot.rtf (was already changed)
		=95 Change patch name CTP =97> PCTE

Done	7. toppar_all36_lipid_lps.str: control characters in old version, test case updated
		=95 New lipid A: ECLIPB
		=95 New lipid A: ECLIPC

Done	8. toppar_all36_na_nad_ppi.str
		=95 Bug fix: ACCE entry for ATP, GTP, CTP, TTP, and UTP

Done	9. [NEW] toppar_all36_lipid_pyrophosphate.str: residues and parameters added to toppar_all36_lipid_miscellaneous.str
		=95 Pyrophosphate lipids (DOPP1, DOPP2, DOPP3, POPP1, POPP2, POPP3)
                alex: required moving MASS/NONBOND for atom types P3 and P4 to parent na toppar files from toppar_all36_na_nad_ppi.str

Done	10. toppar_all36_lipid_bacterial.str: test case updated
		=95 New lipid: DPPGK

Done	11. gbsw/radius_gbsw.str: The full gbsw directory replaced the gbsw in toppar_jul18. I don't support this and as Wonpil is the gbsw guy I assume that the new versions are correct.
		=95 HSE radii is added

Done	12. [NEW] toppar_all36_lipid_ether.str (from Dr. Klauda): test case updated
		=95 Ether lipids (DHPCE, POPCE, DOPCE, DMPCE, POPEE, DOPEE, DPPEE, DMPEE)

Done	13. drude/toppar_drude_master_protein_2013f.str
		=95 Bug fix: typo in element - MASS    -1 OD30E 15.99900 0
                alex: correction made in drude_toppar_2018_10.tgz version of files to be included with new toppar_jul19

Done	14. toppar_all36_lipid_sphingo.str: test case updated
		=95 New lipid: CER3E

Done	15. toppar_all36_lipid_cholesterol.str: test case updated
		=95 New lipids: CHSD, CHSP

Done	16. toppar_all36_lipid_miscellaneous.str: test case updated
		=95 New lipids: DDOPC, DDOPE, DDOPS, PDOPC, PDOPE

Done	17. par_all36_prot.prm / par_all36m_prot.prm: already added
		=95 Bug fix: missing parameter for NNEU (NH2  CT2  C    N)
                alex: NH2  CT2  C    N        0.0000  1     0.00   ! NNEU

Done    Not in Jumin's original list: toppar_all36_prot_stapling.str
                alex: all patches and parameters added to toppar_all36_prot_modify_res.str and corresponding test case updated.
