Example 6. Build a polypeptide alpha helix with defined side chain chi angles using RIBOSOME.
Create a [filename].rib file as below.
title HELIX
default phi -62.0
default psi -41.0
allh
res ace
res arg chi -60
res asn chi -60
res asp chi -60
res cys chi -60
res gly
res gln chi -60
res glu chi -60
res his chi -60
res ile chi -60
res leu chi -60
res lys chi -60
res met chi -60
res phe chi -60
res pro phi -70
res ser chi -60
res thr chi -60
res trp chi -60
res tyr chi -60
res nme
Then give the following command:
python $LINUS24/utils/ribosome.py -p $LINUS24/utils/ribosome.dat < [filename].rib > [filename].pdb
Note: The commard argument -p $LINUS24/utils/ribosome.dat is optional. This specifies which Z-matrix definition of the
amino acid residues to use in constructing the model. Ribosome will use its default Z-matrix if this is not specified.
View the resulting structure file using your favorite molecular graphics program or use it as input to a LINUS24 simulation.
Example 7. Build a polypeptide beta sheet with type II beta turn between HIS and ILE using RIBOSOME.
Create a [filename].rib file as below.
(Notice that we set the CHI values using a single default statement).
title STRAND
default phi -139.0
default psi 135.0
default chi -60.0
allh
res ace
res ala
res arg
res asn
res asp
res cys
res gly
res gln
res glu
res gly phi -60 psi 120
res ala phi 80 psi 0
res leu
res lys
res met
res phe
res pro
res ser
res thr
res trp
res tyr
res val
res nme
Then give the following command:
python $LINUS24/utils/ribosome.py < [filename].rib > [filename].pdb
View the resulting structure file using your favorite molecular graphics program or use it as input to a LINUS24 simulation.
Example 8.
Analyse residue-residue contacts in structures saved during LINUS24 simulation using CONTACT.
This example creates a list of each pair of residues which are in contact in the structures saved in the [filename].out file.
Also included in the list is the fraction of structures in which they in contact.
Residues which were never in contact are not listed.
We will use the output from a simulation of the 20 residue hairpin turn made in Example 7 above.
After simulation of this structure (called hp.pdb here) we have a file of the saved structures in hp.out.
To list the residues that have at least one atom within 1.5 Å (surface to surface) of another residue enter the command:
python $LINUS24/utils/concnt.py hp.pdb hp.out 5 15 1.5
And the output is:
2 7 0.020
5 12 0.020
10 19 0.020
11 19 0.140
12 19 0.040
12 20 0.020
13 19 0.060
14 19 0.780
Example 9.
To allow only certain residues to sample different conformations and keep others fixed in their respective conformations LINUS can read a movelist file at the start of the simulation.
The movelist file is a two column file containing the residue index numbers in the first column and a boolean indicator for each residue in the second column: 0 = fixed, 1 = allow moves.
For example, suppose you had an 18 residue fragment, starting from the extended conformation and you wanted only to sample conformations of the central 4 residues to test for beta-hairpin formation. You would make the following file called movelist,
0 0
1 0
2 0
3 0
4 0
5 0
6 0
7 0
8 1
9 1
10 0
11 0
12 0
13 0
14 0
15 0
16 0
17 0
18 0
19 0
and uncomment the appropriate two lines in your linus.py file,
# mlfile = None
mlfile = os.path.abspath('movelist')
os.link('movelist', curdir+os.sep+'movelist')
Notice that there are lines for residue indices 0 and 19; these are for the ACE and NME.
Also, only postions 8 and 9 are allowed to move when we want the central four residues to move.
Remember that LINUS has a 3 residue moveset so when residue 8 is chosen as the "move" residue, three residues (7, 8, 9) are actually sampling different conformations.
