-
Notifications
You must be signed in to change notification settings - Fork 0
/
README
774 lines (495 loc) · 43.3 KB
/
README
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
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
DDPT
Quick Install:
0. `chmod u+x configure.sh`
1. `./configure.sh` (or `bash configure`)
2. `make`
3. `make install` (`sudo` if you have not selected a local path)
4. Enjoy!
This toolbox has been tested with:
gfortran > 4.4.1
ifort > 11.1
Help:
Help for all programs is available by using the -help tag
when running the program. These help messages are listed at
the end of this file.
For problems with the code please contact thomas.rodgers(at)durham.ac.uk
DDPT: A Comprehensive Toolbox for the Analysis of Protein Motion
Copyright (C) Thomas Rodgers and David Burnell 2012
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Please note the use of Trajutils and Foul within this toolbox which hold
their own GNU General Public Licenses. Please see trajutils.f90 and
foul.f90 for these
G E N E N M M
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program produces the Hermitian matrix for a ENM based on the pdb
inputed with -pdb. A matrix.sdijf file is produced which can be
diagonalised using DIAGSTD to calculate the eigenvalues and vectors.
This program also outputs a map of the spring connections, ENM.vmd which
can be viewed using VMD, and a pdb of the Ca atoms only, CAonly.pdb
Usage:
genENM -pdb pdbfile [-c cut-off] [-f force] [-ccust cfile]
[-fcust ffile] [-spcust spfile] [-mass] [-ca]
[-lig1] [-res] [-het] [-hin] [-hine h] [-an p]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-c Input,Opt 12 Cut-off for spring connectivity
-f Input,Opt 1 Spring constant
-ccust Input,Opt Allows custom cutoffs read from cfile
-fcust Input,Opt Allows custom spring constants read
from ffile
-spcust Input,Opt Allows custom springs to be included
-mass Opt Uses actual atom masses
-ca Opt Calculates Ca model only
-lig1 Opt Assigns each residue in the HETATMs one
average point, only works with -het and
-ca flags as well
-res Opt Assigns ca atom the whole residue mass,
only works with -ca flag as well
-het Opt Includes reading HETATM records
-hin Opt Uses Hinsen fitted interactions
-hine Input,Opt Uses Hinsen exponential interactions
instead, h is the decay factor
-an Input,Opt Uses anisotropic interactions instead,
p is the order of the power decay
-back Input,Opt Strengthens backbone CA atoms by a
factor of b
-dna Opt Reads pdbs that contain DNA, includes
-dna Opt C4 and C1' atoms if -ca is used
cfile format:
WRITE(cfile,'(A4,1X,F7.3)') atomname, cutoff
atomname is in pdb format
e.g.
| C 8.000
| N 8.000
ffile format:
WRITE(ffile,'(1X,I4,1X,A1,1X,I4,1X,A1,1X,F8.3)')
res1, chain1, res2, chain2, kij
res is the residue numbers, chain is the chain code.
res2 can be * which means all connections with res1
e.g.
| 34 A 24 A 3.0
| 329 A * B 3.0
N.B. this will only set connections if within cutoff
spfile format:
WRITE(spfile,'(2(1X,I4,1X,A1))') res1, chain1, res2, chain2
res is the residue numbers. chain is the chain associated with res
e.g.
| 34 A 24 B
| 329 C 124 D
N.B. this will only set connections regardless of cutoff
D I A G S T D
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the normal modes for a ENM based on the reduced
Hermitian matrix file, matrix.sdijf, produced from the ENM program.
A matrix.eigenfacs file is produced which can be further analysed using
the programs in this toolbox.
Usage:
diagstd [-i matrix]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.sdijf reduced Hermitian matrix file
D I A G R T B
VERSION 1.0
Written by:
This program calculates the normal modes for a ENM using the rotational
translational block method based on the reduced Hermitian matrix file,
matrix.sdijf, produced from the ENM program.
The ENM can be split by residues, by the secondary structure (SECO) using
the HELIX and SHEET comands in the pdb, or by custom domains (DOMN) read
from input.domain file.
A matrix.eigenfacs file is produced which can be further analysed using
the programs in this toolbox.
Usage:
diagrtb -pdb pdbfile [-i matrix] [-r num] [-str option]
[-mass] [-het] [-e num] [-high] [-eig] [-mat]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file
-i Input,Opt matrix.sdijf Reduced Hermitian matrix file
-r Input,Opt 1 Number of residues per block
-str Input,Opt NONE Substructuring options, NONE, SECO,
or DOMN
-mass Opt Use true atom masses
-res Opt Use atom residue mass
-het Opt Also read HETATM records
-e Input,Opt 56 Number of eigenvectors output
-eig Opt Print eigenvalues for RTBs
-mat Opt Print RTB matrix
-covar Opt Run with covar matrix input
input.domain format:
WRITE('input.domain','(I4,1X,A1,1X,I4,1X,I4)') domb, cdom, doms, dome
atomname is in pdb format
e.g.
| 1 A 10 15
| 2 B 20 30
D I A G V A L
VERSION 1.0
Written by:
Igors Dubanevics
This program calculates the normal modes for a ENM based on the reduced
Hermitian matrix file, matrix.sdijf, produced from the ENM program.
A matrix.eigenvals file is produced which can be further analysed using
the programs in this toolbox. Can only be used by FREQEN.
Based on DIAGSTD module. Writes only eigenvalues and ommits egeinvectors.
Usage:
diagval [-i matrix]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.sdijf reduced Hermitian matrix file
G N M P R O D
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the normal modes for a GNM based on the pdb
inputed with -pdb. A matrix.eigenfacs file is produced which can be
further analysed using the programs in this toolbox.
This program also outputs a map of the spring connections, GNM.vmd which
can be viewed using VMD, a representation of the pdb in 2d, flat.pdb, and
a pdb of the Ca atoms only, CAonly.pdb.
Usage:
GNM -pdb pdbfile [-c cut-off] [-f force] [-het]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-c Input,Opt 12 Cut-off for spring connectivity
-f Input,Opt 1 Spring constant
-het Opt Include HETATM references with flag
F R E Q / E N
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the normal mode frequencies, output in
mode.frequencies, from an eigenfacs formated file which can be produced
from the included ENM code, GNM code, and the GroAMED packages.
This program also outputs the energy parameters for the normal modes,
output in mode.energy. The value of the partition function, Z; the
full harmonic free energy, G; the Schlitter free energy, Gs; the full
harmanic entropy, S; and the Schlitter entropy, Ss, are given for each
mode.
Usage:
frequency [-i infile] [-t temperature]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.eigenfacs Eigenvector file name
-t Input,Opt 298 Temperature of entropy calculation
-s Input,Opt 1 First eigenvalue included
-e Input,Opt 1000 Last eigenvalue included
N M W I Z W T
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program creates a file suitable for use with the VMD plugin NMWiz,
output as nmwix.nmd, from an eigenfacs formated file which can be
produced from the included ENM code, GNM code, GroNM, GroED, or AmberED
packages. It also requires the matching pdb and the mode.bfactors file
produced with the rms program.
Usage:
w_nmwiz [-i infile] [-pdb pdbfile] [-n numberofmodes]
[-b bfactorfile] [-het]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.eigenfacs Eigenvector file
-pdb Input,Opt CAonly.pdb PDB filename
-n Input,Opt 25 Number of modes written
-b Input,Opt mode.bfactors Calculated bfactor file
-het Opt Incudes reading HETATM records with flag
C R O S C O R
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the average residue cross correlation from an
eigenfacs formated file which can be produced from the included ENM
code, GNM code, or the GroAMED packages.
The output file, crosscor.dat can be plotted in gnuplot with the command:
splot "crosscor.dat" using 1:2:3 notitle
Usage:
cross_cor -i infile [-s startvec]
[-e endvec] [-d1] [-het]
Option Type Value Description
------------------------------------------------------------
-i Input First eigenvector file
-s Input,Opt 7 First included eigenvector number
-e Input,Opt 31 Last included eigenvector number
-d1 Opt Allows 1d vectors with flag
-het Opt Incudes reading HETATM records with flag
R M S / C O L
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the RMSD of each of the atoms for each mode,
output in rms.val, from an eigenfacs formated file which can be produced
from the included ENM code, GNM code, or the GroAMED package.
This program also outputs the collectivity of each mode, output in
collectivity.val.
This program also calculates the predicted bfactors and compares them
with the experimental values given in the original pdbfile, output in
mode.bfactors.
Usage:
rms [-i infile] [-pdb pdbfile] [-s startvec]
[-e endvec] [-d1] [-het]
Option Type Value Description
------------------------------------------------------------
-i Input,Opt matrix.eigenfacs First eigenvector file
-pdb Input,Opt CAonly.pdb pdb file
-s Input,Opt 7 First included eigenvector number
-e Input,Opt 31 Last included eigenvector number
-d1 Opt Allows 1d vectors with flag
-het Opt Incudes reading HETATM records with flag
G R O A M E D
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program converts the output from gromacs g_covar, gromacs g_nmeig,
and amber ptraj commands into files that are compatable with this
toolbox. For gromacs, the eigenvec.trr file needs to be converted into a
readable format using gromacs:
gmxdump -f eigenvec.trr > eigenvec.out
This file can then be input using the -i flag.
The average pdb file produced by gromacs is also needed with the original
pdb file that was used. The eigenval.xvg produced by gromacs is also
used.
A matrix.eigenfacs file is outputted with a pdb file of the Ca atoms,
CAonly.pdb
Usage:
GroAMED -i infile -mdpdb mdpdb -pdb originalpdb
[-eigen eigenfile] [-lig ligand] [-nofit] [-ca]
[-mass resmass]
Option Type Value Description
------------------------------------------------------------
-i Input CA ouputfile
-mdpdb Input MD output pdbfile
-pdb Input Original pdb file
-eigen Input,Opt eigenval.xvg Generated eigenvalue file
-lig Input,Opt NONE Name of any ligand included
-nofit Opt Use if no fitting was used in gromacs
-ca Opt Use if only Ca atoms were fit in gromacs
-mass Input,Opt 99.466 Average residue mass for rescaling if
-ca is used
-nm Opt Use normal mode data instead of PCA data
P L O T P D B
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program copies values for each residue into the bfactor position
in a pdb, if Ca only pdb then the values will be assigned to each Ca
atom, if a full pdf then the values will be assigned to each residue. It
adjusts the second chain assuming that the same residue starts, the
offset can be adjusted with -o num.
overlap.dat contains the overlap of each atom and sum.dat contains the
average values for the whole system.
Usage:
plotpdb -i infile -pdb pdbfile [-het] [-o offset]
Option Type Value Description
------------------------------------------------------------
-i Input Res data file |resnumber value| no header
-pdb Input pdbfile
-het Opt Incudes reading HETATM records with flag
-o Input,Opt 0 Value of the offset if needed
C O V A R
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the covarience matrix from a trajectory and
outputs an eigenfacs type file of the eigenvalues and eigenvectors which
can be further analysed using the rest of this toolbox. The input
trajectories that can be used are:
.prmtop parameter file and .mdcrd trajectory files from amber
.gro parameter file and gmx_dump written trajectory file from gromacs
.CONFIG parameter file and .HISTORY trajectory file from dl_poly
Output files:
average.pdb - average coordinates of the trajectory
rmsd.dat - the rmsd displacement of the atoms from the average
matrix.sdijf - the covarience matrix, only with -mat option
fiteigen.dat - the trajectory coordinates dot product with the
eigenvectors
Usage:
covar -form filetype -p parameterfile -i trajectoryfile
[-ca] [-res] [-s startframe] [-e endframe]
[-skip n] [-mat] [-chain chain.dat]
Option Type Value Description
------------------------------------------------------------
-form Input Input file types: amber, gromacs, dl_poly
-p Input Parameter file: .prmtop, .gro, CONFIG
-i Input Trajectory file: .mdcrd, gmx_dump, HISTORY
-ca Opt Only uses Ca atoms
-res Opt Takes the mass of the residue for the Ca
mass in the analysis, only works with -ca
-s Input,Opt 1 First frame included from the trajectory
-e Input,Opt 100000 Last frame included from the trajectory
-skip Input,Opt 1 Take every n frames
-mat Opt Output the covar matrix, matrix.sdijf
-chain Input,Opt File to list the atoms in each custom user
chain
-sv Input,Opt 1 First eigenvector included in plot
-ev Input,Opt 3 Last eigenvector included in plot
F U L L 2 C A
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program converts any imput files to the versions with only the
alpha Carbon atoms included.
Usage:
genENM -pdb pdbfile [-c cut-off] [-f force] [-ccust cfile]
[-fcust ffile] [-mass] [-ca] [-res] [-het] [-hin h]
[-an p]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-i Input,Opt Convert the eigenfacs style file
-bfac Input,Opt Convert the mode.bfactors file
-het Opt Includes reading HETATM records
D O M A I N S
VERSION 1.0
Written by:
This program rewrites a pdbfile in order of the domains listed in
input.domain for use with rtb domains.
This program also rewrites the domain eigenfacs file back into the
pdb order.
Usage:
domains -pdb pdbfile [-i matrix]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file
-pdb2 Input,Opt domains.pdb Domain ordered pdb file
-i Input,Opt matrix.eigenfacs Domain ordered eigenfacs file
-het Opt Include reading HETATM records
-rev Opt Sort eigenfacs file instead of pdb
input.domain format:
WRITE('input.domain','(I4,1X,A1,1X,I4,1X,I4)') domb, cdom, doms, dome
atomname is in pdb format
e.g.
| 1 A 10 15
| 2 B 20 30
P R O J E C T
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program projects the eigenvectors onto the pdb file
Usage:
genENM -pdb pdbfile [-i eigenfacsfile] [-s start]
[-e end] [-scale n] [-het]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-i Input,Opt matrix.eigenfacs eigenvectors file
-s Input,Opt 7 first eigenvector included
-e Input,Opt 31 last eigenvector included
-scale Input,Opt 1 scale factor
-het Opt include HETATMs
E G N P R O J
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program performs a projection on the eigenspace defined by
precalculated eigenvectors and outputs a plotable file over the number of
specified trajectories.
The input trajectories that can be used are:
.prmtop parameter file and .mdcrd trajectory files from amber
.gro parameter file and gmx_dump written trajectory file from gromacs
.CONFIG parameter file and .HISTORY trajectory file from dl_poly
Usage:
eigen_proj -form filetype -p parameterfile -i trajectoryfile
-pdb pdbfile -eigen eigenfacs [-ca] [-s startframe]
[-e endframe] [-sv startvector] [-ev endvector]
[-skip n]
Option Type Value Description
------------------------------------------------------------
-form Input Input file types: amber, gromacs, dl_poly
-eigen Input Eigenvectors eigenfacs file name
-pdb Input Average pdb structure matching eigenfacs
-p Input Parameter file: .prmtop, .gro, CONFIG
-i Input Trajectory file: .mdcrd, gmx_dump, HISTORY
-ca Opt Only uses Ca atoms
-s Input,Opt 1 First frame included from the trajectory
-e Input,Opt 100000 Last frame included from the trajectory
-skip Input,Opt 1 Take every n frames
-sv Input,Opt 1 First eigenvector included for analysis
-ev Input,Opt 3 Last eigenvector included for analysis
P D B D I F F
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program projects the eigenvectors onto the pdb file
Usage:
genENM -pdb pdbfile [-i eigenfacsfile] [-s start]
[-e end] [-scale n] [-het]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-i Input,Opt matrix.eigenfacs eigenvectors file
-s Input,Opt 7 first eigenvector included
-e Input,Opt 31 last eigenvector included
-scale Input,Opt 1 scale factor
-het Opt include HETATMs
S P A C I N G
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program produces a file, dist.dat for plotting the spacing between
atoms.
Usage:
spacing -pdb pdbfile [-ca] [-het] [-lig1]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-ca Opt Calculates Ca model only
-lig1 Opt Assigns each residue in the HETATMs one
average point, only works with -het and
-ca flags as well
-het Opt Includes reading HETATM records
M O V E I N G
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the change in the distance between atoms between
the equilibrium value and the value after applying the eigenvectors.
The output file, movement.dat, can be plotted in gnuplot with the
command:
splot "moving.dat" using 1:2:3 notitle
Usage:
movement -pdb pdbfile -i eigenfacs file [-s start]
[-e end]
Option Type Value Description
------------------------------------------------------------
-pdb Input pdb file name
-i Input Eigenvector file name
-s Input,Opt 7 First eigenvalue included
-e Input,Opt 31 Last eigenvalue included
T R A J P D B
VERSION 1.0
Written by:
Tom Rodgers and David Burnell
This program calculates the covarience matrix from a trajectory and
Usage:
covar -form filetype -p parameterfile -i trajectoryfile
[-ca] [-res] [-s startframe] [-e endframe]
[-skip n]
Option Type Value Description
------------------------------------------------------------
-form Input Input file types: amber, gromacs, dl_poly
-p Input Parameter file: .prmtop, .gro, CONFIG
-i Input Trajectory file: .mdcrd, gmx_dump, HISTORY
-ca Opt Only uses Ca atoms
-res Opt Takes the mass of the residue for the Ca
mass in the analysis, only works with -ca
-s Input,Opt 1 First frame included from the trajectory
-e Input,Opt 100000 Last frame included from the trajectory
-skip Input,Opt 1 Take every n frames
-box Input,Opt 3 box type used
-pbc Opt Use pbcs
-sol Opt Include solvent atoms