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Article ID: 989 - Last Modified:

How can I create a CMS file that can be used in Desmond from a file that contains the entire system, including solvent?

You can create a CMS file from a file that contains the entire system, including solvent, using the System Builder panel in Maestro.

First, if you have a Maestro file (.mae) that contains the property s_ffio_ct_type, you must edit the file and remove this property. If the Maestro file was generated by VMD, you must also delete atoms with PDB atom name pseu (Maestro property s_m_pdb_atom_name).

If the system is in a PDB file, you must run the preprocessing stage of the Protein Preparation Wizard before starting. Maestro can also read files in mol2 format.

You can create the desired file from Maestro in the System Builder panel, as follows.

  1. Import the system into Maestro.
  2. Choose Applications → Desmond → System Builder.
  3. Select the desired solvent model from the Solvent model option menu.
    The solvent you choose should be the one used in the system you imported. If it is not in the option menu, choose any solvent. In this case, the existing solvent is retained but is treated as part of the solute. Do not choose None, because this choice removes solvent altogether.
  4. Select the appropriate box shape.
  5. Set the Box size calculation method to Absolute size.
  6. Enter the box dimensions from the original Maestro file.
    If you imported the structure from a Maestro file, these are recorded as the properties r_chorus_box_axis, where axis is ax, ay, az, bx, by, bz, cx, cy, cz.
  7. Enter a job name and click Run.
    If you are running Maestro on Windows, click the Settings (gear) button instead, and choose a Linux host to run the job on, then click Run.

The CMS file that is generated can now be used with Desmond.

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