Scanning PES ab initio and in MM

Published in �� 19th, 2015

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.

Quantum chemistry information page

Published in �� 19th, 2015

Posted by comcon1 in ��

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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.

Using Firefly/GAMESS-US efficiently

Published in �� 30th, 2015

Posted by comcon1 in ��

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Here we introduce several hooks that improove calculation speed. 1) Using GUESS=MOREAD and other «continuators» to fast continue broken calculation. 2) Using delocalized coordinates and Z-matrix to improove geometry optimization convergency. 3) Preoptimization with pure basis set and theory level.

Building and plotting Fukui function with FireFly and PyMol

Published in �� 28th, 2014

Posted by comcon1 in ��

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Fukui functions shows the level of reactivity of different places in a complex molecule. They can be easily plotted with GabEdit software but it has a pure functions of chemical drawing. PyMol is a powerful drawing instrument and here we show how to plot Fukui function with PyMOL after two calculation steps with FireFly (PC-GAMESS).

Visualize partial charges in PyMol

Published in �� 30th, 2014

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With QM software like GAMESS/Firefly it is possible to obtain much information about a molecule in text format. There exist some ?envelope? software like Gabedit or WxMacMolPlt that could help you to visualize this information. Here we provide some instructions that will allow you to make your own visualization using powerful abilities of PyMol. Below […]

Using spherical functions (from A.Granovsky manual)

Published in �� 9th, 2014

Posted by comcon1 in ��

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The manual to FireFly program clearly explain why and how to use spherical or cartesian functions when working with different basis sets. Here we publish this part of manual. The fresh and whole manual you can find at the FireFly website, it is free for download and is very useful for both Firefly users and […]

Using RESP with GAMESS-US and Firefly (PC-GAMESS)

Published in �� 16th, 2012

Posted by comcon1 in ��

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To build topology for the new molecule partial charges for atoms should be determined. Working in OPLS force field big amount of atom types with predefined partial charges allows you to chose atom type for almost every atom of your ?new? compound. But In rest force fields you have no choice except use quantum chemistry […]

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