Change Log
  • Changes in version 1.0.0 (2015-04-17)
  • Version 1.0.0 is the first release of CGenFF (i.e. CGenFF is no longer beta), supporting a sufficiently large majority of drug-like molecules to be used routinely in Computer-Aided Drug Design projects. Specifically, it improves upon 0.9.7.1 by introducing support for a number of important functional groups and improving support for a number of moieties. This is largely thanks to improvements in version 3.0.1 of the CGenFF force field, on which it is based. The following is a detailed list of changes:
  •   Introduced support for "bipyrrole-type" sp2-sp2 single bonds between 5-membered rings
  • "Bipyrrole-type" sp2-sp2 single bonds between 5-membered rings commonly occur in drug-like molecules, and represented a major shortcoming in the beta versions of the CGenFF program. Specifically, version 0.9.7 and older produced a qualitatively incorrect representation for compounds containing this motif, which was addressed somewhat unsatisfactory in 0.9.7.1 by rejecting these compounds outright. A true solution to the problem would necessarily involve the introduction of new atom types in the underlying force field, a condition that is now satisfied with the introduction of the types CG2R57 and NG2R57 in CGenFF 3.0.1 . It should be noted that this force field release only contains 3 relevant model compounds; more comprehensive coverage is in the making. That said, errors in the output of release 1.0.0 of the program are expected to be small, especially relative to previous versions.
  •   Fixed bug where in rare cases, atoms were incorrectly recognized as "bipyrrole-type"
  •   Introduced support for "bipyridine-type" nitrogen-containing single bonds between 6-membered aromatic rings
  • Although far smaller in magnitude, the problem with "bipyridine-type" nitrogen-containing single bonds between 6-membered aromatic rings was conceptually similar to the case of the "bipyrrole-type" sp2-sp2 single bonds between 5-membered rings discussed above. The solution was also the same, namely the introduction of a new atom type in CGenFF 3.0.1 - in this case NG2R67 .
  •   Greatly improved nonbonded representation of terminal alkynes
  • Until now, terminal alkynes were not explicitly supported by the underlying force field, resulting in less-than-ideal nonbonded interactions. This was addressed in CGenFF 3.0.1 with the introduction of the new atom type CG1T2 and the change of the terminal alkyne hydrogen atom to HGPAM1 .
  •   New support for bicarbonates/hemicarbonates, sulfamate anions, sulfamides and isocyanates
      Improved support for semi-flexible 5-membered rings and gamma-lactones, non-amide carbonyls in 6-membered aromatic rings, heteroaromatic bicycles and biphenyls, thioether substitutions on heterocycles, taurine amides, N-benzylamides, 1-alkyl-1,2,3-triazoles and phosphoramidates
  • As above, these improvements are the results of continuous extension of the CHARMM General Force Field; again, see the CGenFF changelog for version 3.0.1.
  •   Improved support for neutral sulfamates
  • This is an enhancement of the CGenFF atom typer's support for a functional group that was introduced in version 2b8 of the force field / 0.9.7 of the program.
  •   Substantial improvements in charges on aromatic heterocycles
  • CGenFF version 3.0.1 contains a large number of new heteroaromatic rings and bicycles, which were included in the training set for the charge assignment in version 1.0.0 of the CGenFF program. Physically modest improvements in the assignment of parameters by analogy are also expected.
  •   Reduced numerical noise in charge assignment
  • This is the result of a significant bugfix in the bond charge increment fitting code.
    • Changes in version 0.9.7.1 beta (2014-03-14)
    • Version 0.9.7.1 is a minor bugfix release based on version 2b8 of the CGenFF force field, the same as for 0.9.7. The following is a detailed list of changes:
    •   Fixed atom typing bug in 5-membered ring lactones
    • All 5-membered ring lactones were given a wrong carbonyl carbon atom type. Although the flagrant error is corrected, it should be noted that 5-membered ring lactones are still weakly supported in CGenFF 2b8; this will be addressed in a future release of the force field. We thank CGenFF user Chakrapani Kalyanaraman for reporting this bug.
    •   Explicit warning message for fullerene-like structures
    • It has been reported that, although fullerenes in version 0.9.7 minimize to a correct structure (with a slightly too small diameter), they would undergo unphysical conformational changes during MD. To address this issue, we now changed the atom type on the fullerenes. As a side effect, the diameter has become even smaller (though still not disastrous). To hilight this, fullerenes have been given a warning indicating that they are not explicitly supported. We thank CGenFF user Christian Schönbeck for reporting this bug and for the helpful discussion.
    •   Explicit warning messages for sulfuric and sulfonic acids and bisulfate anions
        Explicit warning message for amidinium resonance in 6-membered aromatic ring
    • Introduced warnings to make it clear that these functional groups are not explicitly supported.
    •   Reject molecules with unsupported bipyridine-type inter-aromatic bond
        Reject molecules with unsupported bipyrrole-type carbons and nitrogens
    • Bipyridine and bipyrrole-type inter-aromatic bonds are unsupported in CGenFF 2b8. Version 0.9.7 of the CGenFF program produced a qualitatively incorrect representation; to prevent this from causing trouble, 0.9.7.1 rejects these structures altogether. Parametrization efforts for these functionalities have been started, so they will presumably be supported in the next CGenFF version.
      • Changes in version 0.9.7 beta (2013-09-04)
      • Version 0.9.7 is mainly a "monster bugfix release", in which we got rid of almost all user-reported and self-discovered issues that accumulated over the last 2 years of beta testing. Additionally, we added support for a few important functional groups that were introduced in version 2b8 of the CGenFF force field. The following is a detailed list of changes:
      •   Support for release 2b8 of the CHARMM General Force Field
      • The output of version 0.9.7 of the CGenFF program should only be used with the new 2b8 release of the CHARMM General Force Field, which can be downloaded at the CGenFF download page. Please refer to the force field's changelog (on the same page) for more info.
      •   New support for saturated 4-membered rings
          Improved support for epoxides, aliphatic nitro groups, neutral organic sulfonates, sulfamates, benzoic acid esters and derivatives
      • These improvement are the result of our ongoing extension of the CHARMM General Force field mentioned above; again, see the CGenFF changelog for version 2b8.
      •   Better charge (and parameter) assignment on positive amines
      • Two separate issues with the charge assignment on positive amines were identified in beta versions <=0.9.6 and fixed in 0.9.7. We recommend our users to resubmit positive amines to the new CGenFF version and compare the charges and parameters by analogy.
      •   Residue IDs (RESI) now truncated at 6 characters for improved compatibility
      • We discovered that Residue IDs with more than 6 characters (as generated by beta version 0.9.6) were problematic for some software, so we now truncate at 6 characters.
      •   Fixed penalty score for ranking resonance structures
      • The coefficients in eq. 2 in [1] were changed from (4, 2, 2, 1) to (8, 4, 3, 2) during development of the CGenFF program, as discussed on p. 3147 of the above reference. This change accidentally did not make it into beta version 0.9.6, but is now present in 0.9.7. The resulting improvement in the resolution of resonance functionality will in some cases lead to more correct atom types, parameters and charges, as well as better guessing of bond orders from the connectivity. Note that despite the improvements, the latter remains a guessing process and will still not yield correct results 100% of the time.
      • [1] K. Vanommeslaeghe, A. D. MacKerell Jr., J. Chem. Inf. Model. 2012, 52, 3144-3154.
      •   Better guessing of bond orders sulphur and phosphorus-containing moieties
      • This improves the reliability of atom typing of these moieties when some of their bonds are marked as aromatic, even if the "guess bond orders" option was not selected. Again, it still will not be 100% correct 100% of the time; for example, in rare cases, sulfinimides may still get typed incorrectly.
      •   Better aromaticity perception on some sulfur-containing rings
      • The presence of a tetrahedrally coordinated sulfur atom or sulfoxide now destroys the aromaticity of potentially aromatic rings.
      •   More sophisticated aromaticity perception algorithm
      • The improved code can handle more complicated cases such as pyranopyran and a number of related user-submitted molecules.
      •   Improved parameter assignment on systems with more than 2 conjugated aliphatic rings
      • Rare instances were reported where systems with more than 2 conjugated aliphatic rings received catastrophically bad angle parameters in beta versions <=0.9.6. This is now cured by improving the penalties for assignment of parameters and charges by analogy.
      •   Correct atom typing when given incorrect bond orders on nitro groups, negative carmabates
      • We identified common mistakes in the bond orders popular molecular editors assign to nitro groups and negative carmabates, and made sure these groups are identified correctly nevertheless.
      •   Corrected atom typing on sulfoximines, phosphorimidates, sulfenates
      •   Fixed formal charge on positively charged bridging nitrogens conjugated to another nitrogen
      • Molecules containing a nitrogen atom that bridges 2 rings and is partially positively charged because it is involved in an amidinium-type resonance were given an incorrect formal charge of +2 in beta versions <=0.9.6 . Examples are the conjugated acid of 1,2,4-triazolo[4,3-a]pyridin-3(2H)-one ( CAS # 6969-71-7 ) and its N1-substituted derivatives such as ZINC17107877 . This is now fixed. Note that correct formal charge assignment does not mean the partial charges on such molecules will be of high quality.
      •   Maximum number of atoms increased to 384
      • To accommodate users studying cavitands, it is now possible to submit molecules up to 384 atoms, but there is a new restriction on the size of the largest aromatic subgraph. In practice, this restriction can only be triggered by graphenes, nanotubes and fullerenes, for which separate tools should be used. We are planning to release one such tool that is fully compatible with the current CGenFF functionality soon; please contact us if you're interested.
      •   Fixed atom renumbering
      • In rare cases, the renumbering algorithm for atoms with the same name still produced duplicate atom names in beta version 0.9.6. This is now fixed.
      •   "Penalty" is now uppercase when including parameters that are already in CGenFF
      • This will presumably make it easier to visually distinguish between existing parameters and new parameter that were assigned by analogy.
      •   Clearer warning messages about sulfinamide and sulfurous diamide not being explicitly supported
      •   Tweaked warning and error messages for nitrates
      •   Miscellaneous tweaks in assignment of charges and parameters by analogy
      • Apart from the aforementioned large modifications affecting positive amines, the penalties for assignment of charges and parameters for some other moieties have been tweaked to a lesser degree. Modest improvements are especially expected in fused and substituted rings. Note that parameters and charges are expected to be generally better in 0.9.7 even if their penalties are now higher; see this FAQ entry.

      • Changes in version 0.9.6 beta (2011-10-06)
      •   Support for release 2b7 of the CHARMM General Force Field
      • The output of version 0.9.6 of the CGenFF program should only be used with the 2b7 release of the CHARMM General Force Field, which can be downloaded at the CGenFF download page. Please refer to the force field's changelog (on the same page) for more info.
      •   Improved accuracy for ketals, neutral enamines and beta-substituted enals
      • This is the result of our ongoing extension of the CHARMM General Force field mentioned above; Again, see the CGenFF changelog for version 2b7.
      •   More accurate parameters and penalties for substituted planar rings and conjugated double bonds
      • After months of beta testing, it was discovered that in some cases, molecules with substituted planar rings or conjugated double bonds yielded unreasonable parameters with misleadingly low penalties. This turned out to be a fundamental shortcoming in the parameter assignment algorithm, necessitating the implementation of substantial new functionality, which is now available in version 0.9.6. The problem was especially pronounced for angle parameters in substituted planar 3- and 5-membered rings. If you have encountered incorrect behavior in such molecules, or molecules with conjugated double bonds, it is advisable to submit the affected compounds to the current version, and contact us if the problem persists or if anything else is odd.
      • That said, note that the new version will often yield different parameters with substantially higher penalties. This is normal and does not imply that the old parameters were more accurate; on the contrary, it means that the penalties for these parameters were too low in the old version, and that after adjusting them upwards, better (ie. lower-penalty) parameters turned out to be available.
      •   "Guess bond orders from connectivity" feature
      • It has been brought to our attention that some popular free molecular editors (most noteworthy VMD) produce mol2 files with invalid bond orders. Also, distorted pdb files are frequently submitted, causing OpenBabel to guess the bond orders incorrectly. To work around these problems, the new version of the interface features a check box to instruct the program to discard input bond orders and guess the bond orders from the connectivity. We would like to stress that this feature should be used with extreme caution! Ordinarily, the program checks whether the input bond orders are consistent with the connectivity, and returns an error if this is not the case. Doing so has already caught many problems that would otherwise lead to incorrect parameters. However, this check is disabled by choosing "guess bond orders..." This implies that if, for instance, hydrogen atoms are missing or placed incorrectly, the program may output grossly inaccurate parameters without warning. Additionally, guessing bond orders may not always work on 3rd-row and heavier elements.
      •   Improved atom typing of polyaromatic heterocycles
      • In some cases, polyaromatic heterocycles containing positive nitrogen atoms and/or carbonyl groups received incorrect atom types. This bug is fixed in version 0.9.6.

      • Changes in version 0.9.1 beta (2011-01-24)
      •   Improved functionality for renumbering atoms with duplicate names
      • The renumbering algorithm in version 0.9.0 in rare cases behaved incorrectly. A new renumbering algorithm that is rigorously correct was implemented.
      •   Minor improvements in the warning and error messages
      • Among other minor changes, unknown triple-bound carbon types now trigger an error message.
      •   Minor improvements in the treatment of spiro compounds