LESSON 1: Calculation of Molconn-Z Structure Reports for Small Molecules

  1. Invoke SYBYL

    2. To begin this lesson, type source $MCONN_DEMO at the unix cshell system prompt. This cshell script makes a new directory in your account titled "mconn4.0S_demo" which has soft links to the master Molconn-Z tutorial directory. Type cd mconn4.0S_demo to change to this new tutorial directory. Then enter the command sybyl to load and run SYBYL.

  2. Analysis of Small Molecules using SYBYL .mol2 files

    3. From the menubar go to the File pulldown and select the Read... command. A list of available files in the current directory appears in the dialog box. If you select Molecule from the File Type menu, the directory list will be filtered (by filename extension) to include only files that are likely to be molecular data. Select cocaine.mol2 and press the OK button. The COCAINE molecule should be displayed in the SYBYL M1 molecular display area.

    Now, pulldown eslc to MolconnZ; select Structure Report... This invokes the MolconnZ Report Dialog box. Select the Atoms... to be operated on. In the Atom Expression dialog box verify that M1 is the chosen molecular area and press the All push button to select all atoms of COCAINE. Press OK. (We will not change the default settings for the Molconn-Z calculational parameters as presented in the Algorithm Options dialog.) This dialog lists selection options for blocks of data to be written to the Structure Report. Select on (for example) Molecule Details, HBond Donors and Acceptors, and Molecular Rings. Enter a filename, i.e., cocaine.rpt for the Report output and press OK.

    Examine the resulting "cocaine.rpt" file if you wish.

    Repeat the calculation for some of the other molecules in the tutorial directory. Note that these molecules have been modeled with specific ionization states (e.g., cocaine salt, aspirin ion). This is a feature of this software that has to be recognized in certain situations where the specific ionization state is unknown, or may be in an equilibrium where more than one state may be in significant concentration.