forked from tbereau/peptideB
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathRELEASE_NOTES
140 lines (115 loc) · 5.6 KB
/
RELEASE_NOTES
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
***********************
* *
* peptideB *
* Tristan Bereau *
* (2008) *
* *
***********************
RELEASE_NOTES :
===============
* Oct 01, 2009:
- Hamiltonian replica exchange has now been implemented. Example file in
examples/polyala.tcl.
* Sep 22, 2009:
- STRIDE has been added to packages/.
- RAGTIME can now take into account Periodic Boundary Conditions when
computing hydrogen bonds.
* Sep 10, 2009:
- added packages/ folder containing both Ragtime and Native_contacts.
- deleted scripts/ folder
- moved configs/ folder to examples/.
* Sep 09, 2009:
- myconfig.h added.
- environment variables (e.g. PEPTIDEB_DIR) more natually used in
peptidebuilder.tcl and .espressorc
* Jul 09, 2009:
- No more 'espresso_switch' variable. Replaced by 'espresso'.
- Started implementing '-randequilib' -- choose random dihedrals
according to an equilibrated structure (ramachandran maps).
* Jun 15, 2009:
- Measurement of observables improved.
* May 5, 2009:
- Hydrophobic environment support. Still need to tune parameters.
* Mar 10, 2009:
- Automatically stop the simulation once any order parameter has reached
a certain threshold.
- Use David Stone's script qparammod.sh to calculate native interactions
in a peptide, by using the command line argument CONTACT{1,2} (one can
define two independent contact order parameters).
* Nov 6, 2008:
- peptideB is now coupled to the ragtime.tcl script. When invoking the
argument -ragtime L where L is a 1-letter code (either A for
alpha-helix or B for beta-sheet) that will store the ratio of selected
conformation as a function of time.
* Oct 7, 2008:
- Electrostatics has been implemented using Debye-Hueckel potentials.
A second version of the MJ coefficients have been implemented for that
purpose.
- Parameter optimization has been removed.
- Somehow there are still problems with display of proteins which are
stretched between two edges of the box...
* Jul 22, 2008:
- Fixed some problems related to confinement of proteins in the
simulation box. They had the tendency to escape ! This seems to be
solved now, but it's not sure...
- The force field is now fixed. It gives very promising results with
folding events of helix bundles and early aggregation events of small
peptides.
* Jun 26, 2008:
- Proline has a specific N bead which doesn't Hbond.
* Jun 10, 2008:
- Starting an implementation of the replica exchange algorithm. It will
only allow as many simulations as processors.
- Analysis of the potential energy.
* May 29, 2008:
- The program is now able to resume a simulation. This does not seem to
work all the time... I should look at it again.
* May 27, 2008:
- [CHANGE] Side chains are now more coarse-grained, less specificity in
their positions and van der Waals radii. The weird dihedral potentials
have been removed.
- Improper dihedral angle now depends on chirality.
* May 14, 2008:
- [NEW] order parameter Q which measures the distance between C_alpha
atoms. This should yield much better results than dihedrals. This can
be turned on by adding '-native FILE' as an argument.
- [NEW] Source parameters in the force field from the configuration file.
* May 13, 2008:
- Brand new force field parameters based on Ramachandran plot
analysis. Van der Waals, temperature, hydrogen bonds, seem to be finely
tuned.
- New pdb startup file. Side chain beads are now explicitely rendered, as
well as their hydrophobicity using a color-code (Blue/Red). There's now
two startup files created, one for displaying the backbone using the
licorice representation and one displaying the structure using
NewCartoon.
* May 8, 2008:
- The parameter optimizer has a new filename, which doesn't include the
year anymore. The overhead now includes the names of the parameters
that are being optimized.
- Implementing specificity on the side chains. They will now have
different strength, position relative to the backbone, and van der
waals radii. The strengths of all the amino acids is controlled by a
single parameter, since we use a hydrophobicity scale to weight the
different attractions between sidechains. Note that even if the code
might refer to beta-carbons, they are all replaced by the center of
mass of the side chain.
* May 7, 2008:
- [CHANGE] Namespace nesting has been redesigned. All functions and
variables now belong to the peptideb namespace. This will be useful once
I combine this script with an upcoming lipid model.
* May 6, 2008:
- [NEW] Output file for parameter optimization. It saves the state in a
file simplex.dat in the current directory. The file has an identifier
that depends on the date.
- [CHANGE] peptidebuilder will not print integration steps when doing
parameter optimization anymore.
* May 5, 2008:
- [NEW] Implementation of the nearest-neighbor dipole interaction by
applying a bias in the dihedral potentials of the angles phi and psi.
* May 2, 2008:
- [NEW] Implementation of the parameter optimizer.
- The hbond potential was capped in order not to misbehave in very rare
configurations. The capping can be set in src/chain_interactions.tcl
using the ::HBond_max_cap variable. It looks like 100.0 is a good
number for now.