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exercises:2015_cecam_tutorial:forcefields

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exercises:2015_cecam_tutorial:forcefields [2015/09/01 21:45]
mwatkins
exercises:2015_cecam_tutorial:forcefields [2015/09/02 05:07] (current)
mwatkins
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   {{http://​www.cp2k.org/​_media/​exercises:​2015_cecam_tutorial:​vmd_solvate.png}}   {{http://​www.cp2k.org/​_media/​exercises:​2015_cecam_tutorial:​vmd_solvate.png}}
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-Now you should have solvate.psf and solvate.pdb in your directory, which contain the coordinates and connectivity information of the solvated protein. For some proteins you might now need to add ions into the solvent to neutralize the system, but we're OK with ubiquitin.+Now you should have solvate.psf and solvate.pdb in your directory, which contain the coordinates and connectivity information of the solvated protein. Open the .psf file edit the first line to simple read PSF. For some proteins you might now need to add ions into the solvent to neutralize the system, but we're OK with ubiquitin.
  
 At this point we're nearly ready to run CP2K. First we need to get hold of the forcefield files. The CHARMM forcefields are distributed from the MacKrell group website {{http://​mackerell.umaryland.edu/​charmm_ff.shtml}}. Download toppar_c31b1.tar.gz,​ extract it with something like tar -zxvf toppar_c31b1.tar.gz. ​ At this point we're nearly ready to run CP2K. First we need to get hold of the forcefield files. The CHARMM forcefields are distributed from the MacKrell group website {{http://​mackerell.umaryland.edu/​charmm_ff.shtml}}. Download toppar_c31b1.tar.gz,​ extract it with something like tar -zxvf toppar_c31b1.tar.gz. ​
exercises/2015_cecam_tutorial/forcefields.txt ยท Last modified: 2015/09/02 05:07 by mwatkins