- Create a clean directory in your home directory. This is where you put all the files needed.
- Copy there:
- the CHARMM force field parameter and topology files. A force field is a mathematical expression of the potential which atoms in the system feel. The parameter file sets bond strengths, equilibrium lengths, etc. The topology file contains information on atom types, charges and how the atoms are connected in a molecule. (Note that the pdb file contains only coordinates, but not connectivity information).
- your PDB file containing the atomic coordinates. Make sure the chain identifiers are correct.
- Prepare a file moleman.csh to align the axes of inertia with the orthogonal frame. Run it (source moleman.csh). If all goes well there are two new files (moleman.log, aligned.pdb).
- If your molecule contains more than one chain, create seperate pdb files, each containing coordinates of a single chain, with the correct chain identifier.
- Prepare a file psfgen.csh to generate a psf file (protein structure file), which stores structural information of the protein, such as varius types of bonding interactions, and a pdb file containing guessing coordinates for missing atoms. Run it (source psfgen.csh).
- Determine the limits of the system via pdbset from the CCP4 suite of program. (pdbset xyzin ionised.pdb >& pdbset.log)
- Prepare a NAMD minimization and heating-up script.
- Create a directory at /work/md/ .
- Copy here the necessary files, that is:
- the ionized pdb and psf files
- the force field parameter file
- the NAMD script
- the fix_backbone and restrain_ca pdb files
- Create an output subdirectory, where NAMD output files will be written.
- Create the NAMD.sh, the parallel NAMD job submission script.
- qsub NAMD.sh to submit your job.
- Create a heat directory and move all the files there. Create an equi directory.
- Copy from heat/output the following:
- heat_out.coor
- heat_out.vel
- heat_out.xsc
- Copy from heat/ the following:
- the ionized pdb and psf files
- the force field parameter file
- Create an output subdirectory, where NAMD output files will be written.
- Create a NAMD equilibration script.
- Create the NAMD.sh submission script.
- qsub NAMD.sh to submit your job.
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