Analyze ligand geometries using the Cambridge Structural Database (CSD): Difference between revisions
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Chasemwebb (talk | contribs) (Created page with "Often, it is useful to determine if a torsion or conformer is not energetically favourable. This can be accomplished from an ab initio QM calculation but in the Shoichet Lab, ...") |
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Written by Chase Webb 20190521 | |||
The generation of torsion angle distributions to determine conformational preference about single rotatable bonds is one of the most common uses of the CSD. This tutorial illustrates how '''Mogul''', part of the CSD software can be used to rapidly determine the torsion angle preferences of substituted oxamides by inspecting occurrences of this motif in the CSD. | |||
Source the current environment for CSD-2019 | |||
source /nfs/soft/csd/csd-2019/env.csh | |||
Open mogul it by running the following command: | |||
/nfs/soft/csd/csd-2019/CSD_2019/bin/mogul | |||
If prompted for the license, it lives here: | |||
/nfs/soft/csd/csd-2019/CSD_2019/csd_licence.dat | |||
In the CCDC Mogul 1.8.1 interface, import smiles by clicking load, or draw the motif you are interested in assessing by clicking on the Draw button to bring up a drawing window. | |||
Revision as of 21:53, 21 May 2019
Written by Chase Webb 20190521
The generation of torsion angle distributions to determine conformational preference about single rotatable bonds is one of the most common uses of the CSD. This tutorial illustrates how Mogul, part of the CSD software can be used to rapidly determine the torsion angle preferences of substituted oxamides by inspecting occurrences of this motif in the CSD.
Source the current environment for CSD-2019
source /nfs/soft/csd/csd-2019/env.csh
Open mogul it by running the following command:
/nfs/soft/csd/csd-2019/CSD_2019/bin/mogul
If prompted for the license, it lives here:
/nfs/soft/csd/csd-2019/CSD_2019/csd_licence.dat
In the CCDC Mogul 1.8.1 interface, import smiles by clicking load, or draw the motif you are interested in assessing by clicking on the Draw button to bring up a drawing window.