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#27250 - 04/18/11 04:18 PM Re: CGenFF version 2b6; CGenFF program available [Re: Kenno]
Kenno Offline
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Registered: 12/19/05
Posts: 1535
Loc: Baltimore, MD
Originally Posted By: Kenno
If VMD complies with the aforementioned mol2 standard, it should work (and these guys are pretty competent so I expect it will).
I have to retract that statement; on closer inspection, it is very difficult to create a mol2 file with acceptable bond orders using VMD. frown

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#28443 - 10/13/11 12:38 AM Re: CGenFF version 2b6; CGenFF program available [Re: Kenno]
Kenno Offline
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Registered: 12/19/05
Posts: 1535
Loc: Baltimore, MD
CGenFF 2b7 can now be downloaded from the CGenFF download page as well as the MacKerell lab's force field page. This is a minor update, issued mainly for compatibility with the new version 0.9.6 of the CGenFF program. Here is an incremental list of changes since CGenFF version 2b6 (copy-pasted from the download page):
  • 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

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#32541 - 09/05/13 02:43 PM CGenFF version 2b8 [Re: Kenno]
Kenno Offline
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Registered: 12/19/05
Posts: 1535
Loc: Baltimore, MD
CGenFF 2b8 can now be downloaded from the MacKerell lab's force field page. It introduces support for a few important functional groups, contains a number of fixes, and is compatible with the new version 0.9.7 beta of the CGenFF program at paramchem.org. Here is an incremental list of changes since CGenFF version 2b7 (copy-pasted from the CGenFF download page):
  • 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)
  • 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

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#34932 - 04/20/15 02:53 PM CGenFF out of beta: version 3.0.1 ! [Re: Kenno]
Kenno Offline
Forum Member

Registered: 12/19/05
Posts: 1535
Loc: Baltimore, MD
CGenFF 3.0.1 can now be downloaded from the MacKerell lab's force field page. This 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, and is compatible with the new version 1.0.0 of the CGenFF program at paramchem.org. Here is an incremental list of changes since CGenFF version 2b8 (copy-pasted from the CGenFF download page):

  • 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)


Edited by Kenno (04/20/15 02:58 PM)
Edit Reason: introduced circular intra-forum reference :-P

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