Pdb2torenergy example

From victor
Jump to: navigation, search

Trying with a PDB file that contains more than one chain

 ./pdb2torenergy -i ../samples/2FGW.pdb --allchains -p

The output would be as shown:

1       0.000000      (first residue from the first chain)
2       0.072441      (second residue from the first chain)
3       -0.401921
4       -2.234889
...
210     -0.014719
211     0.570740
212     0.270957       (last residue from the first chain)
1       0.000000       (first residue from the second chain)
2       -0.168721      (second residue from the second chain)
3       0.609889
....
210     -0.014719
211     0.570740
212     0.270957
1       0.000000
2       -0.168721
3       0.609889      (last residue from the second and last chain)


By the other side, if no residue detail is needed, but want to consider each chain, you should use the command:

./pdb2torenergy -i ../samples/2FGW.pdb --allchains -v


As the verbose mode was activate (-v), the output would be:

../samples/2FGW.pdb	 -77.7668		L	size: 214
../samples/2FGW.pdb	 -46.4044		H	size: 220

If you need to evaluate an NMR PDB file, you just need to use:

./pdb2torenergy -i ../samples/2MKP.pdb -c C -v --nmr

The verbose output would be:

../samples/2MKP.pdb mod. 1	 -14.7970		C	size: 89
../samples/2MKP.pdb mod. 2	 -10.5857		C	size: 89
....
../samples/2MKP.pdb mod. 9	 -15.5181		C	size: 89
../samples/2MKP.pdb mod. 10	 -10.0480		C	size: 89