OPLS-AA topology generation is a very complex task because of huge amount of the atomtypes described this force field. The OPLS-AA force filed contains more than 800 atom types that is nevertheless not sufficient for describing all the diversity of chemical structures. Thus, as parameters for new chemical fragments appears in literature the atomtype database […]

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Here is the tutorial about how to scan potential energy over specific internal coordinate (e.g. dihedral angle) ab initio and then transfer this trajectory into molecular mechanics package and compare them.

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On this page we collect references to our resources, documentation and resources on other sites. All these data are very helpful for everybody who wants to learn practical quantum chemistry.

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FRAP kinetics can be measured from image series directly with numpy libraries. However sometimes it is necessary to remove motion of the sample before measuring fluorescence intensity. In such a case it is possible to use normalized cross-correlation technique. Here we provide script that helps you to remove sample motion and obtain FRAP kinetics from […]

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