DESMOND

Desmond

• opt/ shrodinger2019-1/ Schrodinger.host file setting:

  • 
    

# Local workstation

name: myhostname

host: localhost

processors: 12

tmpdir: /usr/tmp

gpgpu: 0, Tesla K40

• • 
    

• System Preparation:

  • Align our model to the OPM protein using the following command in Pymol:

    • 
      

align modelName, OPMfileName

• • Save the aligned model.

  • File -> Export Molecular -> Selection modelName -> Save

  • Import the aligned model in Maestro.

  • Prepare using Protein Preparation under Tasks. Add hydrogen and cap termini. Click Preprocess.

  • Select the prepared structure from the table. Export the prepared structure as a .mae file.

  • Reopen Maetro and import the OPM file (a .pdb file) and the prepared structure (a .mae file).

  • Perform a molecular dynamics simulation by going to tasks -> System builder.

  • Go to 'Set Up Membrane' and change POPC to POPE, select 'Place on Prealigned Structure'. Click OI.

  • Change the solvent model 'SPC' to 'TIP3P'.

  • Under the Ions tab, you may also add salts . A common choice is 0.150 mol NaCl.

  • Once all of the settings are chosen, click Run. It may take a few minutes.

• Membrane Relaxation:

  • $SCHRODINGER/run -FROM desmond viparr.py -f tip3p_charmm -f charmm27 6msm.cms 6msm_Charmm.cms

  • $SCHRODINGER/run -FROM desmond build_constraints.py 6msm_Charmm.cms 6msm_md.cms

  • $SCHRODINGER/run relax_membrane.py 6msm_md.cms -t 310 -j membrane

  • $SCHRODINGER/utilities/multisim -JOBNAME membrane -cpu 10 -i membrane-in.cms -m membrane.msj -o membrane-out.cms

    • There are 12 cpus in computer 3, we use 10 of 12.