![]() Next, the atomic coordinates are taken from the same PDB file (if some atoms are different between our new structure and the PDB file we use for coordinates, we will receive a warning). Notice the brackets-these brackets define the PSF generation. Then we read the primary sequence from the PDB file ‘1pgb_new.pdb’. ![]() In general, ANY name can be used here, but it should be descriptive. Line by line, we label a segment as ‘main’ (main will contain the whole protein. The ‘pdbalias’ command renames a particular carbon atom to one that our simulation software will recognize. Topology top_all27_prot_lipid.rtf #this loads the topology library fileĪfter loading the topology file, you may see a bunch of warning messages scroll by. Package require psfgen #loads the PSF generation package Now, examine this PDB file you just wrote out (you can do this by entering ‘more 1pgb_new.pdb’. $pgb writepdb 1pgb_new.pdb #Writes the coordinates out Set pgb # variable assignment - only the protein, no waters, etc Remember that everything after the hash "#" character is a comment and is not processed. This is not always necessary, but it is good programming practice to keep one command per line. NOTE: for the most part, these lines should be entered as written here: after each line hit. Let’s assume that we are going to download 1PGB from RCSB, and eventually run a simulation on it. We will use the small leucine zipper that we examined earlier. Put it in your main class directory so you can find it easily. Find it HERE, or get it from the FILES PAGE. To prepare, we will need the topology file (top_all27_prot_lipid.rtf).
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |