Download the new CGenFF tutorial (tgz archive)
that was presented at CECAM's June 2012 and 2013 "Advances in Biomolecular Modelling and Simulations using CHARMM" workshops
. This tutorial is fully up-to-date with recent developments, most importantly the availability of the CGenFF program
, and the usage of 3-point scans to determine the force constant for select bonds, angles and improper dihedrals in larger model comounds. It largely skips the details about the target data generation steps and instead focuses more on the details of the actual force field optimization. Special thanks go to Jonathan Chee Yang Loh, whose contributions are marked "jon" in the tutorial files.
Download the accompanying slide show (recommended!)
The first part of this presentation is about the (then) state of the art of the CHARMM force field; please skip to slide 76 for the actual tutorial.
Download the old CGenFF tutorial (tgz archive)
that was included as supporting information with the CGenFF paper
. This tutorial is somewhat outdated, but is still of value because it goes into a little bit more detail concerning the target data generation than the new tutorial.
Note: the CGenFF topology and parameter files included in these tutorials cannot be assumed to be up-to-date! For production calculations, download the latest CGenFF version!
New CGenFF version
Version 4.0 of the CGenFF topology and parameter files (2016-08-16) is integrated in the latest release of the CHARMM additive force field. It is not compatible with the current version (1.0.0) of the CGenFF program at paramchem.org , but version 2.0 of the program is coming soon and will provide compatibility with this version (4.0) of the force field.
Latest CGenFF version
version 3.0.1 is the first release of CGenFF (i.e. CGenFF is no longer beta). It improves upon 2b8 by introducing support for a number of important functional groups and improving support for a number of cyclic moieties. It is compatible with version 1.0.0 of the CGenFF program at paramchem.org .
Changelog (changes from version 2b8 to 3.0.1):
- Introduced basic support for "bipyrrole-type" sp2-sp2 single bonds between 5-membered rings through new atom types CG2R57 and NG2R57 ; more fine-grained support in the making
- Added terminal alkyne model compound (RESI PRPY) with new atom type CG1T2 and associated parameters (contribution by Madhurima Jana); tweaked disubstituted alkyne 2BTY
- Added support for sulfamate anion; tweaked CG331 NG2S3 parameter based on X-ray survey, which also improves phosphoramidates (RESI PHA)
- Added support for sulfamide (contributed by Ting Ran)
- Added model compound N-acetyltaurine and parameters, and reintroduced taurine patch for bile acids
- Introduced basic isocyanate support; tweaked CG2O7 OG2D5 to be a compromise between isocyanate X-ray survey data and CO2
- Extended support for "biphenyl" inter-aromatic single bonds to heterocycles, including "bipyridine-type" bonds through the new atom type NG2R67 (contribution by Ignacio Soteras Gutiérrez)
- Added semi-flexible 5-membered rings cyclopentene (contributed by Madhurima Jana), oxolan-2-one, 5H-furan-2-one and 3H-furan-2-one (RESI CYPE GBL B2FO A2FO , respectively) and parameters
- Added a series of heteroaromatic rings and bicycles (contributed by Ignacio Soteras Gutiérrez)
- Added basic support for azide-alkyne Huisgen cycloaddition "click chemistry" products through model compound 1-ethyl-1,2,3-trizaole and parameters
- Added support for methylthio substituents on heterocycles (contribution by Ignacio Soteras Gutiérrez)
- Added model compound N-benzylacetamide and parameters (contributed by Ignacio Soteras Gutiérrez)
- Added bicarbonate model compound and parameters
- Renamed RESI AP2 to APNH, TP2 to PNH2 and PRES SAHC to SAH to avoid naming conflicts with CHARMM36 residues
- Fixed wrong ACCE record in RESI ATP (does not influence the energetics)
Older CGenFF versions
Note: as CGenFF is still actively growing and being improved, using older CGenFF versions is not recommended for any purpose except reproducing old calculations.
Version 3.0.0 was only distributed to a few privileged parties. From an energetic point of view, it is 100% identical to 3.0.1 . The only differences are:
- its topology file mistakenly lacked the taurine patch for bile acids, which we promised to reintroduce in the 3.0 release;
- residue ANPHM in 3.0.0 was renamed to NZAD in 3.0.1 ;
- a few comments were changed.
See the change log for version 3.0.1
version 2b8 is an update of 2b7 that introduces support for a few important functional groups and contains a number of fixes. It is compatible with versions 0.9.7 and 0.9.7.1 beta of the CGenFF program at paramchem.org .
Changelog (changes from version 2b7 to 2b8):
- Introduced support for common saturated 4-membered rings through the model compounds cyclobutane (RESI CBU) and 2-azetidinone (RESI AZDO) and the new atom types CG3C41 and NG2R43
- Added epoxide model compounds and parameters (RESI 1EOX and 1BOX and atom type OG3C31; contributed by Sherry (Hua) Chen)
- Added support for benzoic acid esters and derivatives through RESI ZOIC and MBOA
- Added support for aliphatic nitro groups through RESI NIME and NIPR
- Added sulfamate model compounds and parameters (RESI MSMT and PSMT)
- Expanded support for neutral organic sulfonate through RESI PMST
- Corrected wrongly transfered dihedral parameters for the hydroxyl hydrogen atom in alcohols - many compounds affected (problem reported by Xibing He)
- Added model compounds for the drug hydrochlorothiazide: RESI OBTZ and APBT
- Slight tweak of charges on RESI DMBU to fix minor inconsistency
- Slight tweak in the following sulfonyl bond lenghts to improve agreement with crystal data: NG311-SG3O2, NG321-SG3O2, OG303-SG3O2
- Fixed former "slack" dihedral parameter HGR62 CG2R62 NG2R61 HGP1 to improve hydrogen wagging in the vibrational spectrum of aromatic heterocycles
- Improved transferability of CG2O5 CG311 OG311 angle
- Improved transferability of OG2D2 CG2O3 CG311 CG2R61 dihedral
- Fixed multiplicity problem for X CG311 NG2R53 CG2R53 dihedrals
- Reserved MASS numbers for nearly-finished parametrization projects on terminal alkynes, azides, bipyrroles and hydroxamic acids
- Modified a number of comments
version 2b7 is a minor update of 2b6 to make the force field compatible with version 0.9.6 beta of the CGenFF program at paramchem.org . Specifically, the introduction of 4 new atom types for 5-membered rings with exocyclic double bonds was required.
Changelog (changes from version 2b6 to 2b7):
- Introduced 4 new atom types for 5-membered rings with exocyclic double bonds such as fulvene and azaprotoanemonin. This was necessary for compatibility with the improved assignment of substituted 5-membered ring parameters by analogy in version 0.9.6 of the CGenFF program.
- Added basic ketal model compounds and parameters (RESI DMOP and DMBU)
- Added basic neutral enamine model compound and parameters (RESI AMET)
- Fixed a conjugated double bond parameter for beta-substituted enals
- Fixed H-N-H angle force constant in neutral amines
- Slightly tweaked C-N reference distance in protonated primary amines
- Uniformized dihedral parameters that control wagging motions of 3-substituents on pyridine rings
- Updated charges on RESI 3ACP
version 2b6 is compatible with versions 0.9.0 and 0.9.1 beta of the CGenFF program at paramchem.org . It was released only on the MacKerell lab's force field page
in December 2010.
Changelog (changes from version 2b5 to 2b6):
- Reorganization of improper dihedrals; impropers are now assigned using simple consistent rules and wildcards have been eliminated. Many parameters were tweaked and many compounds changed energy because of this.
- Renumbered atom types following the insertion of two new sulfur types (see below) - old psf files are henceforward invalid
- Added sulfonamide parameters
- Added sulfone parameters
- Added sulfoxide parameters
- Added anionic sulfonate parameters
- Added limited support for sulfonic esters
- Added parameters for ketones conjugated to double bonds and aromatic rings; slight tweak of existing ketone parameters
- Added aliphatic and aromatic amidinium parameters
- Added parameters for acyclic enol ethers
- Fixed more inconsistencies in conjugated double bond parameters - in particular, cyclic enol ethers should be better-behaved
- Fixed a few minor inconsistencies in torsional paramters for amides of aliphatic carboxylic acids (acetamide, propanamide, butyramide,...)
- Miscellaneous new model compounds:
- p-cyanotoluene (RESI 4CYT)
- trimethylamine N-oxide (RESI TMAO)
- dimethylpropanamide (RESI DMPR)
- pentamidine (RESI PNTM)
- Changed the names of the following residues so that they don't coincide with other CHARMM force fields anymore:
- ALAD → AANM
- GLYP → AAPM
- DMPA → DMEP
- CHL1 → CLOL
- CHNS → CLNS
- CHM1 → CLM1
- Rounded "3rd digit" charges in 3-fluoropyridine (RESI 3FLP) for improved portability
- Updated default nonbonded settings to fshift & vfswitch
version 2b5 was released only on the MacKerell lab's force field page
in August 2010.
Changelog (changes from version 2b4 to 2b5):
- Changed atom typing scheme for phosphates; partial reparameterization of phosphor-oxygen bonds
- Eliminated asymmetric dihedrals and impropers - many compounds affected
- Big purge of "slack" parameters. If you are missing parameters that were present in older versions, please report it on the CHARMM forums. Alternatively, if for some reason you don't feel comfortable with using the forums for this purpose, you can e-mail me (Kenno Vanommeslaeghe)
- Renumbered atom types in the framework of CHARMM force field re-organization - old psf files are henceforward invalid
- Added carbamate parameters (RESI DMCA and DECA)
- Added parameters for styrene (RESI STYR)
- Miscellaneous new model compounds:
- 2-Pyridone (RESI 2PYO) and uracil (RESI URAC)
- 4,6-dioxabicyclo[3.3.0]octan-8-ol (RESI RSRF)
- 1,2,4-Oxadiazole (RESI OXD4)
- RESI HDZ1B, another phenylhydrazone model compound
- methyl triphosphate (RESI METP)
- Updated parameters for 1,2,4-triazole (RESI TRZ4)
- Updated OG312 L-J parameters
- Updated CG2R61 NG311 bond; affected compounds: RESI FEOZ, FETZ
- Fixed inconsistencies in conjugated double bond parameters - many compounds affected
- Fixed an incorrect pyridine parameter - affects most pyridines
- Fixed aniline amide torsion lacking multiplicity 1 term
- Fixed a copy-paste error in a dihedral parameters in RESI DMP2
- Fixed atom types and charges on fluor-substituted THF derivatives (RESI T2FD, T2FU, TMFD, TMFU, THNP)
- Fixed charges on "carbocyclic" nucleotide derivatives (RESI CNGU, CSGU, CNTH, CSTH, CNT1, CNT2, CNT3, CNCY, CSCY)
- Fixed CG2DC? atom types on RESI TMCH (not conjugated)
- Fixed CG2DC? atom types on RESI PRAC, PRAL, HDZ2 (conjugated)
- Fixed atom types on RESI PMHA
- Fixed atom types on RESI 2AMP
- Fixed charges on RESI THF2
- Added missing improper in RESI 3CPY
- Fixed some IC tables
- Removed RESI 4HQI because it was broken while fixing parameters it shares with more important model compounds
- Removed RESI TEAZ, TDAZ because of issues with atom typing that were not trivial to correct - inquire if you need these compounds
- Removed RESI DMSO in preparation of upcoming sulfur reparameterization - inquire if you need it
- Renamed protonated TMAO to RESI TMAOP (neutral TMAO is coming soon; inquire if intersted)
version 2b4 was released with CHARMM version 36a4.
Changelog (changes from version 2b1 to 2b4):
- Introduced carbamate parameters
- Introduced parameters for extended ketones (contributed by Iakov Polyak)
- Added limited thiocarbonyl support
- Added parameters for phenylhydrazine
- Added various other model compounds and parametes
- Updated bonded parameters for -CH2-NH2(+)-CH2 group (somewhat developmental; future tweaks likely)
- Corrected charges in RESI PPI2 topology
- Slight tweak in bonded parameters for benzenes with aliphatic substituents
- Slight tweak in benzamide bonded parameters
- Slight tweak in bonded parameters for sterane scaffold and beta-ionone ring
- Removed slack parameters containing NG2S0
version 2b1 was released only on the MacKerell lab's force field page
in July 2009.
Changelog (changes from version 2a5 to 2b1):
- Fixed atom typing mistakes in cholesterol. Doing so mandated removing and adding a few parameters.
- Updated OCO angle in RESI DIOL.
- Corrected atom types on RESI GABD.
version 2a5 was used for generating the data in the CGenFF paper and the associated (old) tutorial.
Changelog (changes from version 2a0 to 2a5):
- Corrected faulty carbonyl L-J parameters; updated charges on esters, aldehydes and ketones.
- Corrected big mistake in NG311 L-J and updated charges accordingly.
- Finalized alkyne L-J parameters and charges.
- Tweaked L-J on 5-membered ring sp2 carbons.
- Switched ATOM CG2DC1 and ATOM CG2DC2, inserted ATOM CG2D2O and renumbered carbon types.
- Retyped RESI NICH and RESI NDPH.
- Restored "CG321 CG321 CG321 NG2S1" parameter which got deleted accidentally.
- Added RESI CO2.
- Symmetrized C-S-C charges.
- Many more small improvements.
version 2a0 was an early alpha version that was released to a limited audience with CHARMM versions 36a1, 36a2 and 36a3 for the purpose of technical compatibility testing. This version had major issues and is not recommended!!!