#Toppar change log
#Update of the additive CHARMM36 force-field toppar files

*** 2026_2_14

Additional changes associated with version 5.0 of CGenFF. Both the current
version 4.6 and version 5.0 will be made available as follows.

Version 4.6 given the following names. These were already in the
toppar_c36_releases but will be renamed to the following. In addition a v4.6 test case is

top_all36_cgenff_v4.6.rtf
par_all36_cgenff_v4.6.prm

test/test_cgenff_v4.6.inp

Version 5.0 is assummed to be the default

top_all36_cgenff.rtf
par_all36_cgenff.prm

test/test_cgenff.inp: requires test_cgenff_pre_v5.0.str and test_ic_atoms.str

run_all36_test.cmd: updated to run both testcases. requires manual
intervention to set information for charmm version and location.

These changes superseed some of the changes made below.

*** 2026_1_24

Updating of the CGenFF Version5.0 topology and parameter files and the test case
Alex MacKerell

The number of parameters in CGenFF v5.0 is greatly increased,
therefore the following CHARMM Array dimensions need to be set to the
following and the program compiled. This has been done by the
CHARMM-GUI people so their version runs the new CGenFF. Future
versions of CHARMM release will have the correct dimensions.

MAXCP 100000
MAXNBF 400000

Repeated residues when using CHARMM-GUI inputs. These have been
present for a long time and are due to, in part, a lot of residues in
the CHARMM biomolecular force field being included in CGenFF. The way
the toppar files are streamed the CHARMM biomolecular force field
versions of the repreated residues are read after the CGenFF versions
and therefore are the ones being applied if they are generated during
any calculations. In addition, there are a number of repeated
parameters and other warnings. These are largely due to non-MacKerell
toppar files. In all cases the final version of a parameter is the one
used for the calculations.

CGenFF updates, Version 5.0

1) top_all36_cgenff.rtf: minor corrections and update of comments

2) par_all36_cgenff.prm: release parameters, currently v5.0, with
various corrections, charge increment information removed and the
bonded parameters aligned.

Note that some dihedral parameters have 5 significant figures as shown
below. align.sh misses these and they were manually corrected.

CG331  CG321  CG321  CG331      0.03819 2     0.00 ! LIPID alkane, 4/04, jbk, adm2026

3) par_all36_cgenff_increments.prm: release parameters, currently
v5.0, WITH the charge increment terms, various corrections and bonded
parameters NOT aligned

4) Test cases updated to test_cgenff_all.inp. This includes all
pre-version 5.0 tests and the v5.0 tests. The input streams
test_ic_atoms.str and test_cgenff_pre_v5.0.str and test_cgenff_5.0.ene
is written with the energies for all the molecules. see test subdirectory.

! References:                                                                  !
! K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong,               !
!      J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov and               !
!      A. D. Mackerell Jr., J. Comput. Chem. 2010, 31, 671-690. PMC2888302,    !
!      10.1002/jcc.21367                                                       !
!                                                                              !
! W. Yu, X. He, K. Vanommeslaeghe, A. D. MacKerell Jr., J. Comput. Chem. 2012, !
!       33, 2451-2468, PMC3477297, 10.1002/jcc.23067                           !
!                                                                              !
! Croitoru, A., Kumar, A., Lambry, J.C., Lee, J., Sharif, S., Yu, W.,          !
!      MacKerell, A.D., Jr.,* and Alexey Aleksandrov, A.,* JCTC 21: 3044-3065, !
!      2025, PMC11938330, 10.1021/acs.jctc.5c00046                             !


