| How do I analyze a PDB file with multiple entries? |
| Saturday, 10 September 2005 | |||||||||||||
Assuming your .pdb file is called "eiwit.pdb", this is what you would do:
-reth lets pdb2gmx keep all hydrogens which are present in your input file. It will also not add any missing hydrogens, so your molecules should be complete. -ter will cause pdb2gmx to ask for termini types for which you must select 'none' for both C- and N-terminus. -n tells pdb2gmx to generate a .ndx file with the atoms reordered to the GROMACS standard. pdb2gmx now generates a topology file (topol.top) which exactly corresponds with the molecule(s) in your input file. It also writes a coordinate file (conf.gro). The next step is (all this should be on a single line):
Yes, -f eiwit.pdb works because a .pdb is also a trajectory format in GROMACS. -ox sets output to .xtc. -n clean tells trjconv to use the clean.ndx generated by pdb2gmx, so the atom ordering in the output (.xtc) file will be according to GROMACS standards. -timestep 1 sets the timestep between output frames to one, so the structures from the .pdb file get numbered sequentially. -ter causes TER markers in the .pdb file to be seen as end-of-frame, default ENDMDL is used. If you are not sure what is in your eiwit.pdb, TER is a good guess, but you should check. If you have ENDMDL in stead of TER, omit the -ter. -box 10 sets a default box-size in the output .xtc trajectory (since no box is stored in a .pdb file). The size is in nm and should be larger than your molecule size. -center resets the geometrical center of each of your structures to the center of the box (the one you specify with -box). trjconv will generate a .xtc trajectory file with all the coordinates from your eiwit.pdb. A not very exiting but mandatory step is:
This will generate a run input file (topol.tpr) from the topol.top and conf.gro you generated with pdb2gmx. A default grompp.mdp is available. You can probably use it 'as is', but you might want or need to modify some thing. In any case you are encouraged to review the description of the numerous options in the .mdp file. Now, suppose you want to calculate all cross-rmsd values for all structures. Enter:
-f eiwit.xtc and -s topol.tpr are self-explanatory. -m tells g_rms to output an RMSD matrix in .xpm format, which can be directly viewed with for example xv. Of course there are many more analysis tools available. For example ngmx a trajectory viewer. A list of all tools is available in the online manual.
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