How do I analyze a PDB file with multiple entries?
.pdb file is
called "eiwit.pdb", this is what you would do:
pdb2gmx -f eiwit.pdb -reth -ter -n
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
The next step is:
trjconv -f eiwit.pdb -o eiwit.xtc -n clean -timestep 1 -box 10 -center
Yes, -f eiwit.pdb works because a .pdb is also a
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
-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:
grompp -f grompp.mdp -c conf.gro -p topol.top
This will generate a run input file
(topol.tpr) from the
topol.top and conf.gro you generated with
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
g_rms -f eiwit.xtc -s topol.tpr -m
-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