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
|
<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1">
<meta name="theme-color" content="#6a9fb5">
<title>Fixing ADFRSuite for Apple Silicon</title>
<!--
<link rel="stylesheet" href="https://unpkg.com/latex.css/style.min.css" />
-->
<link rel="stylesheet" href="/assets/c-hyde.css" />
<link rel="stylesheet" href="http://fonts.googleapis.com/css?family=PT+Sans:400,400italic,700|Abril+Fatface">
<link rel="stylesheet" href="/assets/main.css" />
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="og:site_name" content="Navan Chauhan" />
<link rel="canonical" href="https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html" />
<meta name="twitter:url" content="https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html" />
<meta name="og:url" content="https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html" />
<meta name="twitter:title" content="Fixing ADFRSuite for Apple Silicon" />
<meta name="og:title" content="Fixing ADFRSuite for Apple Silicon" />
<meta name="description" content="Fixing ADFRsuite on M1/MX chip Macs - CLI Tools" />
<meta name="twitter:description" content="Fixing ADFRsuite on M1/MX chip Macs - CLI Tools" />
<meta name="og:description" content="Fixing ADFRsuite on M1/MX chip Macs - CLI Tools" />
<meta name="twitter:card" content="summary_large_image" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link rel="shortcut icon" href="/images/favicon.png" type="image/png" />
<link rel="alternate" href="/feed.rss" type="application/rss+xml" title="Subscribe to Navan Chauhan" />
<meta name="twitter:image" content="https://web.navan.dev/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png" />
<meta name="og:image" content="https://web.navan.dev/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png" />
<meta name="google-site-verification" content="LVeSZxz-QskhbEjHxOi7-BM5dDxTg53x2TwrjFxfL0k" />
<script data-goatcounter="https://navanchauhan.goatcounter.com/count"
async src="//gc.zgo.at/count.js"></script>
<script defer data-domain="web.navan.dev" src="https://plausible.io/js/plausible.js"></script>
<link rel="manifest" href="/manifest.json" />
</head>
<body class="theme-base-0d">
<div class="sidebar">
<div class="container sidebar-sticky">
<div class="sidebar-about">
<h1><a href="/">Navan</a></h1>
<p class="lead" id="random-lead">Alea iacta est.</p>
</div>
<ul class="sidebar-nav">
<li><a class="sidebar-nav-item" href="/about/">about/links</a></li>
<li><a class="sidebar-nav-item" href="/posts/">posts</a></li>
<li><a class="sidebar-nav-item" href="/3D-Designs/">3D designs</a></li>
<li><a class="sidebar-nav-item" href="/feed.rss">RSS Feed</a></li>
<li><a class="sidebar-nav-item" href="/colophon/">colophon</a></li>
</ul>
<div class="copyright"><p>© 2019-2024. Navan Chauhan <br> <a href="/feed.rss">RSS</a></p></div>
</div>
</div>
<script>
let phrases = [
"Something Funny", "Veni, vidi, vici", "Alea iacta est", "In vino veritas", "Acta, non verba", "Castigat ridendo mores",
"Cui bono?", "Memento vivere", "अहम् ब्रह्मास्मि", "अनुगच्छतु प्रवाहं", "चरन्मार्गान्विजानाति", "coq de cheval", "我愛啤酒"
];
let new_phrase = phrases[Math.floor(Math.random()*phrases.length)];
let lead = document.getElementById("random-lead");
lead.innerText = new_phrase;
</script>
<div class="content container">
<div class="post">
<h1 id="fixing-adfrsuite-for-apple-silicon">Fixing ADFRSuite for Apple Silicon</h1>
<p>We are going to be running everything through Rosetta 2. I am confident that if I had access to the original source code, I could find a way to run everything natively. </p>
<p>These are the following issues that we will be fixing in this part:</p>
<ul>
<li>“python2.7” cannot be opened because the developer cannot be verified.</li>
<li>OpenBabel Error</li>
<li>Segmentation fault while running the <a rel="noopener" target="_blank" href="https://ccsb.scripps.edu/adcp/tutorial-redocking/">redocking tutorial</a></li>
</ul>
<p>For the sake of simplicity, I am assuming that I am running all these commands in the folder <code>~/Developer/scrippstuff/</code></p>
<h2 id="installing-rosetta-2">Installing Rosetta 2</h2>
<p>We are going to run all of these steps in the terminal</p>
<div class="codehilite">
<pre><span></span><code>/usr/sbin/softwareupdate<span class="w"> </span>--install-rosetta<span class="w"> </span>--agree-to-license
</code></pre>
</div>
<h3 id="install-homebrew-for-x86">Install Homebrew for x86</h3>
<p>Both versions of homebrew (x86 and arm64) can peacefully coexist on your system.</p>
<p>From now on, every command should be run in a terminal session that starts with this as the first command:</p>
<div class="codehilite">
<pre><span></span><code>arch<span class="w"> </span>-x86_64<span class="w"> </span>zsh
</code></pre>
</div>
<p>Now, we can install homebrew:</p>
<div class="codehilite">
<pre><span></span><code>/bin/bash<span class="w"> </span>-c<span class="w"> </span><span class="s2">"</span><span class="k">$(</span>curl<span class="w"> </span>-fsSL<span class="w"> </span>https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh<span class="k">)</span><span class="s2">"</span>
</code></pre>
</div>
<p>Here is my output:</p>
<div class="codehilite">
<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>uname<span class="w"> </span>-a
Darwin<span class="w"> </span>Navans-MacBook-Pro.local<span class="w"> </span><span class="m">23</span>.3.0<span class="w"> </span>Darwin<span class="w"> </span>Kernel<span class="w"> </span>Version<span class="w"> </span><span class="m">23</span>.3.0:<span class="w"> </span>Wed<span class="w"> </span>Dec<span class="w"> </span><span class="m">20</span><span class="w"> </span><span class="m">21</span>:31:00<span class="w"> </span>PST<span class="w"> </span><span class="m">2023</span><span class="p">;</span><span class="w"> </span>root:xnu-10002.81.5~7/RELEASE_ARM64_T6020<span class="w"> </span>x86_64
➜<span class="w"> </span>scrippstuff<span class="w"> </span>/bin/bash<span class="w"> </span>-c<span class="w"> </span><span class="s2">"</span><span class="k">$(</span>curl<span class="w"> </span>-fsSL<span class="w"> </span>https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh<span class="k">)</span><span class="s2">"</span>
<span class="o">==</span>><span class="w"> </span>Checking<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="sb">`</span>sudo<span class="sb">`</span><span class="w"> </span>access<span class="w"> </span><span class="o">(</span>which<span class="w"> </span>may<span class="w"> </span>request<span class="w"> </span>your<span class="w"> </span>password<span class="o">)</span>...
Password:
<span class="o">==</span>><span class="w"> </span>This<span class="w"> </span>script<span class="w"> </span>will<span class="w"> </span>install:
/usr/local/bin/brew
/usr/local/share/doc/homebrew
/usr/local/share/man/man1/brew.1
/usr/local/share/zsh/site-functions/_brew
/usr/local/etc/bash_completion.d/brew
/usr/local/Homebrew
<span class="o">==</span>><span class="w"> </span>The<span class="w"> </span>following<span class="w"> </span>new<span class="w"> </span>directories<span class="w"> </span>will<span class="w"> </span>be<span class="w"> </span>created:
/usr/local/Cellar
/usr/local/Caskroom
Press<span class="w"> </span>RETURN/ENTER<span class="w"> </span>to<span class="w"> </span><span class="k">continue</span><span class="w"> </span>or<span class="w"> </span>any<span class="w"> </span>other<span class="w"> </span>key<span class="w"> </span>to<span class="w"> </span>abort:
<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/mkdir<span class="w"> </span>-p<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom
<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/chmod<span class="w"> </span><span class="nv">ug</span><span class="o">=</span>rwx<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom
<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>navanchauhan<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom
<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/bin/chgrp<span class="w"> </span>admin<span class="w"> </span>/usr/local/Cellar<span class="w"> </span>/usr/local/Caskroom
<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>-R<span class="w"> </span>navanchauhan:admin<span class="w"> </span>/usr/local/Homebrew
<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/mkdir<span class="w"> </span>-p<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew
<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/bin/chmod<span class="w"> </span>g+rwx<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew
<span class="o">==</span>><span class="w"> </span>/usr/bin/sudo<span class="w"> </span>/usr/sbin/chown<span class="w"> </span>-R<span class="w"> </span>navanchauhan<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>and<span class="w"> </span>installing<span class="w"> </span>Homebrew...
remote:<span class="w"> </span>Enumerating<span class="w"> </span>objects:<span class="w"> </span><span class="m">47</span>,<span class="w"> </span><span class="k">done</span>.
remote:<span class="w"> </span>Counting<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">47</span>/47<span class="o">)</span>,<span class="w"> </span><span class="k">done</span>.
remote:<span class="w"> </span>Compressing<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">19</span>/19<span class="o">)</span>,<span class="w"> </span><span class="k">done</span>.
remote:<span class="w"> </span>Total<span class="w"> </span><span class="m">47</span><span class="w"> </span><span class="o">(</span>delta<span class="w"> </span><span class="m">28</span><span class="o">)</span>,<span class="w"> </span>reused<span class="w"> </span><span class="m">47</span><span class="w"> </span><span class="o">(</span>delta<span class="w"> </span><span class="m">28</span><span class="o">)</span>,<span class="w"> </span>pack-reused<span class="w"> </span><span class="m">0</span>
Unpacking<span class="w"> </span>objects:<span class="w"> </span><span class="m">100</span>%<span class="w"> </span><span class="o">(</span><span class="m">47</span>/47<span class="o">)</span>,<span class="w"> </span><span class="m">6</span>.11<span class="w"> </span>KiB<span class="w"> </span><span class="p">|</span><span class="w"> </span><span class="m">223</span>.00<span class="w"> </span>KiB/s,<span class="w"> </span><span class="k">done</span>.
From<span class="w"> </span>https://github.com/Homebrew/brew
<span class="w"> </span>+<span class="w"> </span>18ebdd8c8f...67a096fcbb<span class="w"> </span>tapioca-compiler-for-tty-rbi<span class="w"> </span>-><span class="w"> </span>origin/tapioca-compiler-for-tty-rbi<span class="w"> </span><span class="o">(</span>forced<span class="w"> </span>update<span class="o">)</span>
Switched<span class="w"> </span>to<span class="w"> </span>and<span class="w"> </span>reset<span class="w"> </span>branch<span class="w"> </span><span class="s1">'stable'</span>
<span class="o">==</span>><span class="w"> </span>Updating<span class="w"> </span>Homebrew...
<span class="o">==</span>><span class="w"> </span>Installation<span class="w"> </span>successful!
<span class="o">==</span>><span class="w"> </span>Homebrew<span class="w"> </span>has<span class="w"> </span>enabled<span class="w"> </span>anonymous<span class="w"> </span>aggregate<span class="w"> </span>formulae<span class="w"> </span>and<span class="w"> </span>cask<span class="w"> </span>analytics.
Read<span class="w"> </span>the<span class="w"> </span>analytics<span class="w"> </span>documentation<span class="w"> </span><span class="o">(</span>and<span class="w"> </span>how<span class="w"> </span>to<span class="w"> </span>opt-out<span class="o">)</span><span class="w"> </span>here:
<span class="w"> </span>https://docs.brew.sh/Analytics
No<span class="w"> </span>analytics<span class="w"> </span>data<span class="w"> </span>has<span class="w"> </span>been<span class="w"> </span>sent<span class="w"> </span>yet<span class="w"> </span><span class="o">(</span>nor<span class="w"> </span>will<span class="w"> </span>any<span class="w"> </span>be<span class="w"> </span>during<span class="w"> </span>this<span class="w"> </span>install<span class="w"> </span>run<span class="o">)</span>.
<span class="o">==</span>><span class="w"> </span>Homebrew<span class="w"> </span>is<span class="w"> </span>run<span class="w"> </span>entirely<span class="w"> </span>by<span class="w"> </span>unpaid<span class="w"> </span>volunteers.<span class="w"> </span>Please<span class="w"> </span>consider<span class="w"> </span>donating:
<span class="w"> </span>https://github.com/Homebrew/brew#donations
<span class="o">==</span>><span class="w"> </span>Next<span class="w"> </span>steps:
-<span class="w"> </span>Run<span class="w"> </span>these<span class="w"> </span>two<span class="w"> </span>commands<span class="w"> </span><span class="k">in</span><span class="w"> </span>your<span class="w"> </span>terminal<span class="w"> </span>to<span class="w"> </span>add<span class="w"> </span>Homebrew<span class="w"> </span>to<span class="w"> </span>your<span class="w"> </span>PATH:
<span class="w"> </span><span class="o">(</span>echo<span class="p">;</span><span class="w"> </span><span class="nb">echo</span><span class="w"> </span><span class="s1">'eval "$(/usr/local/bin/brew shellenv)"'</span><span class="o">)</span><span class="w"> </span>>><span class="w"> </span>/Users/navanchauhan/.zprofile
<span class="w"> </span><span class="nb">eval</span><span class="w"> </span><span class="s2">"</span><span class="k">$(</span>/usr/local/bin/brew<span class="w"> </span>shellenv<span class="k">)</span><span class="s2">"</span>
-<span class="w"> </span>Run<span class="w"> </span>brew<span class="w"> </span><span class="nb">help</span><span class="w"> </span>to<span class="w"> </span>get<span class="w"> </span>started
-<span class="w"> </span>Further<span class="w"> </span>documentation:
<span class="w"> </span>https://docs.brew.sh
</code></pre>
</div>
<p>At this point, you don't need to edit your <code>zshrc</code> or <code>zsh_profile</code>.</p>
<h3 id="install-pyenv">Install pyenv</h3>
<p>The reason we are installing pyenv is because it is easier to build Python 2.7.18 from scratch than messing around with codesigning and quarantine bs on macOS.</p>
<div class="codehilite">
<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>brew<span class="w"> </span>install<span class="w"> </span><span class="nv">pyenv</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pyenv/manifests/2.3.36
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>dependencies<span class="w"> </span><span class="k">for</span><span class="w"> </span>pyenv:<span class="w"> </span>m4,<span class="w"> </span>autoconf,<span class="w"> </span>ca-certificates,<span class="w"> </span>openssl@3,<span class="w"> </span>pkg-config<span class="w"> </span>and<span class="w"> </span><span class="nv">readline</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">m4</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/blobs/sha256:8434a67a4383836b2531a6180e068640c5b482ee6781b673d65712e4fc86ca76
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">autoconf</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/blobs/sha256:12368e33b89d221550ba9e261b0c6ece0b0e89250fb4c95169d09081e0ebb2dd
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>ca-certificates
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:cab828953672906e00a8f25db751977b8dc4115f021f8dfe82b644ade03dacdb
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>openssl@3
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/blobs/sha256:ef8211c5115fc85f01261037f8fea76cc432b92b4fb23bc87bbf41e9198fcc0f
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span>pkg-config
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/blobs/sha256:421571f340277c62c5cc6fd68737bd7c4e085de113452ea49b33bcd46509bb12
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">readline</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:9796e0ff1cc29ae7e75d8fc1a3e2c5e8ae2aeade8d9d59a16363306bf6c5b8f4
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Fetching<span class="w"> </span><span class="nv">pyenv</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pyenv/blobs/sha256:d117a99ed53502aff29109bfa366693ca623f2326e1e6b4db68fef7b7f63eeba
<span class="c1">############################################################################################################################################################### 100.0%</span>
<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>dependencies<span class="w"> </span><span class="k">for</span><span class="w"> </span>pyenv:<span class="w"> </span>m4,<span class="w"> </span>autoconf,<span class="w"> </span>ca-certificates,<span class="w"> </span>openssl@3,<span class="w"> </span>pkg-config<span class="w"> </span>and<span class="w"> </span><span class="nv">readline</span>
<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">m4</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19
Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/5b2a7f715487b7377e409e8ca58569040cd89f33859f691210c58d94410fd33b--m4-1.4.19.bottle_manifest.json
<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>m4--1.4.19.sonoma.bottle.tar.gz
🍺<span class="w"> </span>/usr/local/Cellar/m4/1.4.19:<span class="w"> </span><span class="m">13</span><span class="w"> </span>files,<span class="w"> </span><span class="m">739</span>.9KB
<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">autoconf</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72
Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/b73cdb320c4261bbf8d02d03e50dc755c869c5859c1d4e93616898fc7cd939ff--autoconf-2.72.bottle_manifest.json
<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>autoconf--2.72.sonoma.bottle.tar.gz
🍺<span class="w"> </span>/usr/local/Cellar/autoconf/2.72:<span class="w"> </span><span class="m">71</span><span class="w"> </span>files,<span class="w"> </span><span class="m">3</span>.6MB
<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>ca-certificates
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11
Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/c431e0186df2ccc2ea942b34a3c26c2cebebec8e07ad6abdae48447a52c5f506--ca-certificates-2024-03-11.bottle_manifest.json
<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>ca-certificates--2024-03-11.all.bottle.tar.gz
<span class="o">==</span>><span class="w"> </span>Regenerating<span class="w"> </span>CA<span class="w"> </span>certificate<span class="w"> </span>bundle<span class="w"> </span>from<span class="w"> </span>keychain,<span class="w"> </span>this<span class="w"> </span>may<span class="w"> </span>take<span class="w"> </span>a<span class="w"> </span><span class="k">while</span>...
🍺<span class="w"> </span>/usr/local/Cellar/ca-certificates/2024-03-11:<span class="w"> </span><span class="m">3</span><span class="w"> </span>files,<span class="w"> </span><span class="m">229</span>.6KB
<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>openssl@3
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1
Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/f7b6e249843882452d784a8cbc4e19231186230b9e485a2a284d5c1952a95ec2--openssl@3-3.2.1-1.bottle_manifest.json
<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>openssl@3--3.2.1.sonoma.bottle.1.tar.gz
🍺<span class="w"> </span>/usr/local/Cellar/openssl@3/3.2.1:<span class="w"> </span><span class="m">6</span>,874<span class="w"> </span>files,<span class="w"> </span><span class="m">32</span>.5MB
<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span>pkg-config
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3
Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/ac691fc7ab8ecffba32a837e7197101d271474a3a84cfddcc30c9fd6763ab3c6--pkg-config-0.29.2_3.bottle_manifest.json
<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>pkg-config--0.29.2_3.sonoma.bottle.tar.gz
🍺<span class="w"> </span>/usr/local/Cellar/pkg-config/0.29.2_3:<span class="w"> </span><span class="m">11</span><span class="w"> </span>files,<span class="w"> </span><span class="m">656</span>.4KB
<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span>pyenv<span class="w"> </span>dependency:<span class="w"> </span><span class="nv">readline</span>
<span class="o">==</span>><span class="w"> </span>Downloading<span class="w"> </span>https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10
Already<span class="w"> </span>downloaded:<span class="w"> </span>/Users/navanchauhan/Library/Caches/Homebrew/downloads/4ddd52803319828799f1932d4c7fa8d11c667049b20a56341c0c19246a1be93b--readline-8.2.10.bottle_manifest.json
<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>readline--8.2.10.sonoma.bottle.tar.gz
🍺<span class="w"> </span>/usr/local/Cellar/readline/8.2.10:<span class="w"> </span><span class="m">50</span><span class="w"> </span>files,<span class="w"> </span><span class="m">1</span>.7MB
<span class="o">==</span>><span class="w"> </span>Installing<span class="w"> </span><span class="nv">pyenv</span>
<span class="o">==</span>><span class="w"> </span>Pouring<span class="w"> </span>pyenv--2.3.36.sonoma.bottle.tar.gz
🍺<span class="w"> </span>/usr/local/Cellar/pyenv/2.3.36:<span class="w"> </span><span class="m">1</span>,158<span class="w"> </span>files,<span class="w"> </span><span class="m">3</span>.4MB
<span class="o">==</span>><span class="w"> </span>Running<span class="w"> </span><span class="sb">`</span>brew<span class="w"> </span>cleanup<span class="w"> </span>pyenv<span class="sb">`</span>...
Disable<span class="w"> </span>this<span class="w"> </span>behaviour<span class="w"> </span>by<span class="w"> </span>setting<span class="w"> </span>HOMEBREW_NO_INSTALL_CLEANUP.
Hide<span class="w"> </span>these<span class="w"> </span>hints<span class="w"> </span>with<span class="w"> </span>HOMEBREW_NO_ENV_HINTS<span class="w"> </span><span class="o">(</span>see<span class="w"> </span><span class="sb">`</span>man<span class="w"> </span>brew<span class="sb">`</span><span class="o">)</span>.
</code></pre>
</div>
<p>And, build the last version of Python 2.7</p>
<div class="codehilite">
<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span><span class="nv">PYENV_ROOT</span><span class="o">=</span><span class="s2">"~/Developer/scrippstuff"</span><span class="w"> </span>pyenv<span class="w"> </span>install<span class="w"> </span><span class="m">2</span>.7.18
python-build:<span class="w"> </span>use<span class="w"> </span>openssl<span class="w"> </span>from<span class="w"> </span>homebrew
python-build:<span class="w"> </span>use<span class="w"> </span>readline<span class="w"> </span>from<span class="w"> </span>homebrew
Downloading<span class="w"> </span>Python-2.7.18.tar.xz...
-><span class="w"> </span>https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz
Installing<span class="w"> </span>Python-2.7.18...
patching<span class="w"> </span>file<span class="w"> </span>configure
patching<span class="w"> </span>file<span class="w"> </span>configure.ac
patching<span class="w"> </span>file<span class="w"> </span>setup.py
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Mac/Tools/pythonw.c'</span>
patching<span class="w"> </span>file<span class="w"> </span>setup.py
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Doc/library/ctypes.rst'</span>
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Lib/test/test_str.py'</span>
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Lib/test/test_unicode.py'</span>
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/_ctypes.c'</span>
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/callproc.c'</span>
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/ctypes.h'</span>
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Modules/_ctypes/callproc.c'</span>
patching<span class="w"> </span>file<span class="w"> </span>setup.py
patching<span class="w"> </span>file<span class="w"> </span><span class="s1">'Mac/Modules/qt/setup.py'</span>
patching<span class="w"> </span>file<span class="w"> </span>setup.py
python-build:<span class="w"> </span>use<span class="w"> </span>readline<span class="w"> </span>from<span class="w"> </span>homebrew
python-build:<span class="w"> </span>use<span class="w"> </span>zlib<span class="w"> </span>from<span class="w"> </span>xcode<span class="w"> </span>sdk
Installed<span class="w"> </span>Python-2.7.18<span class="w"> </span>to<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/~/Developer/scrippstuff/versions/2.7.18
</code></pre>
</div>
<p>Test the new installation:</p>
<div class="codehilite">
<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>~/Developer/scrippstuff/<span class="se">\~</span>/Developer/scrippstuff/versions/2.7.18/bin/python2.7
Python<span class="w"> </span><span class="m">2</span>.7.18<span class="w"> </span><span class="o">(</span>default,<span class="w"> </span>Mar<span class="w"> </span><span class="m">28</span><span class="w"> </span><span class="m">2024</span>,<span class="w"> </span><span class="m">20</span>:47:13<span class="o">)</span>
<span class="o">[</span>GCC<span class="w"> </span>Apple<span class="w"> </span>LLVM<span class="w"> </span><span class="m">15</span>.0.0<span class="w"> </span><span class="o">(</span>clang-1500.1.0.2.5<span class="o">)]</span><span class="w"> </span>on<span class="w"> </span>darwin
Type<span class="w"> </span><span class="s2">"help"</span>,<span class="w"> </span><span class="s2">"copyright"</span>,<span class="w"> </span><span class="s2">"credits"</span><span class="w"> </span>or<span class="w"> </span><span class="s2">"license"</span><span class="w"> </span><span class="k">for</span><span class="w"> </span>more<span class="w"> </span>information.
>>><span class="w"> </span>from<span class="w"> </span>random<span class="w"> </span>import<span class="w"> </span>randint
>>><span class="w"> </span>randint<span class="o">(</span><span class="m">0</span>,10<span class="o">)</span>
<span class="m">6</span>
>>><span class="w"> </span>exit<span class="o">()</span>
</code></pre>
</div>
<p>Now, we can compress this newly created Python version into a <code>tar.gz</code> file to replace the one provided in ADFRsuite<em>x86</em>64Darwin_1.0.tar.gz. Don't forget the <code>.</code> at the end</p>
<div class="codehilite">
<pre><span></span><code>➜<span class="w"> </span>scrippstuff<span class="w"> </span>tar<span class="w"> </span>-C<span class="w"> </span>./<span class="se">\~</span>/Developer/scrippstuff/versions/2.7.18<span class="w"> </span>-czf<span class="w"> </span>new.tar.gz<span class="w"> </span>.
</code></pre>
</div>
<h2 id="install-adfrsuite">Install ADFRsuite</h2>
<p>If you don't already have the tarball, you can download it by:</p>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span>curl<span class="w"> </span>-o<span class="w"> </span>adfr.tar.gz<span class="w"> </span>https://ccsb.scripps.edu/adfr/download/1033/
</code></pre>
</div>
<p>Uncompress it</p>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span>tar<span class="w"> </span>-xvzf<span class="w"> </span>adfr.tar.gz
</code></pre>
</div>
<p>Replace the provided Python archive with the one we created:</p>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADFRsuite_x86_64Darwin_1.0
$<span class="w"> </span>mv<span class="w"> </span>new.tar.gz<span class="w"> </span>Python2.7.tar.gz
</code></pre>
</div>
<p>Note: For some reason simply copying it doesn't work and you need to use <code>mv</code></p>
<p>Just to not mess with anything else, I will be installing everything in a folder called <code>clean_install</code></p>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span>mkdir<span class="w"> </span>clean_install
$<span class="w"> </span>./install.sh<span class="w"> </span>-d<span class="w"> </span>clean_install
...
<span class="w"> </span>ADFRsuite<span class="w"> </span>installation<span class="w"> </span>complete.
To<span class="w"> </span>run<span class="w"> </span>agfr,<span class="w"> </span>agfrgui,<span class="w"> </span>adfr,<span class="w"> </span>autosite,<span class="w"> </span>about,<span class="w"> </span>pythonsh<span class="w"> </span>scripts<span class="w"> </span>located<span class="w"> </span>at:
/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin
add<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin<span class="w"> </span>to<span class="w"> </span>the<span class="w"> </span>path<span class="w"> </span>environment<span class="w"> </span>variable<span class="w"> </span><span class="k">in</span><span class="w"> </span>.cshrc<span class="w"> </span>or<span class="w"> </span>.bashrc:
.cshrc:
<span class="nb">set</span><span class="w"> </span><span class="nv">path</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin<span class="w"> </span><span class="nv">$path</span><span class="o">)</span>
.bashrc:
<span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:<span class="nv">$PATH</span>
</code></pre>
</div>
<p>Now, to test <code>agfr</code>, first run the command (replacing <code>navanchauhan</code> with yout username)</p>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span><span class="nb">export</span><span class="w"> </span><span class="nv">PATH</span><span class="o">=</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:<span class="nv">$PATH</span>
$<span class="w"> </span>agfr
➜<span class="w"> </span>ADFRsuite_x86_64Darwin_1.0<span class="w"> </span><span class="nv">agfr</span>
<span class="o">==============================</span>
***<span class="w"> </span>Open<span class="w"> </span>Babel<span class="w"> </span>Error<span class="w"> </span><span class="k">in</span><span class="w"> </span>openLib
<span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so<span class="w"> </span>did<span class="w"> </span>not<span class="w"> </span>load<span class="w"> </span>properly.
<span class="w"> </span>Error:<span class="w"> </span>dlopen<span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so,<span class="w"> </span>0x0009<span class="o">)</span>:<span class="w"> </span>Library<span class="w"> </span>not<span class="w"> </span>loaded:<span class="w"> </span>/opt/X11/lib/libcairo.2.dylib
<span class="w"> </span>Referenced<span class="w"> </span>from:<span class="w"> </span><24174F3E-2670-79AC-4F26-F8B49774194A><span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so
<span class="w"> </span>Reason:<span class="w"> </span>tried:<span class="w"> </span><span class="s1">'/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/opt/X11/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/local/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/lib/libcairo.2.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file,<span class="w"> </span>not<span class="w"> </span><span class="k">in</span><span class="w"> </span>dyld<span class="w"> </span>cache<span class="o">)</span>
<span class="o">==============================</span>
</code></pre>
</div>
<h2 id="fixing-open-babel-error">Fixing <code>Open Babel Error</code></h2>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span>brew<span class="w"> </span>install<span class="w"> </span>cairo
</code></pre>
</div>
<h2 id="completing-the-re-docking-tutorial">Completing the re-docking tutorial</h2>
<h3 id="dowbloading-the-dataset">Dowbloading the dataset</h3>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span>curl<span class="w"> </span>-o<span class="w"> </span>tutorial-data.zip<span class="w"> </span>https://ccsb.scripps.edu/adcp/download/1063/
$<span class="w"> </span>unzip<span class="w"> </span>tutorial-data.zip
$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADCP_tutorial_data/3Q47
</code></pre>
</div>
<h3 id="conversion-to-pdbqt">Conversion to PDBQT</h3>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span>reduce<span class="w"> </span>3Q47_rec.pdb<span class="w"> </span>><span class="w"> </span>3Q47_recH.pdb
$<span class="w"> </span>reduce<span class="w"> </span>3Q47_pep.pdb<span class="w"> </span>><span class="w"> </span>3Q47_pepH.pdb
</code></pre>
</div>
<h3 id="preparing-receptor">Preparing Receptor</h3>
<pre><code>$ prepare_receptor -r 3Q47_recH.pdb
$ prepare_ligand -l 3Q47_pepH.pdb
</code></pre>
<h3 id="generate-target-file">Generate Target File</h3>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47
➜<span class="w"> </span>3Q47<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47
Traceback<span class="w"> </span><span class="o">(</span>most<span class="w"> </span>recent<span class="w"> </span>call<span class="w"> </span>last<span class="o">)</span>:
<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">36</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module>
<span class="w"> </span>from<span class="w"> </span>ADFR.utils.runAGFR<span class="w"> </span>import<span class="w"> </span>runAGFR
<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">41</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module>
<span class="w"> </span>from<span class="w"> </span>ADFR.utils.maps<span class="w"> </span>import<span class="w"> </span>flexResStr2flexRes
<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">35</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module>
<span class="w"> </span>from<span class="w"> </span>ADFRcc.adfr<span class="w"> </span>import<span class="w"> </span>GridMap
<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">34</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module>
<span class="w"> </span>from<span class="w"> </span>ADFRcc.adfr<span class="w"> </span>import<span class="w"> </span>Parameters
<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">43</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module>
<span class="w"> </span>import<span class="w"> </span>ADFRcc.adfrcc<span class="w"> </span>as<span class="w"> </span>CPP
<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">28</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span><module>
<span class="w"> </span><span class="nv">_adfrcc</span><span class="w"> </span><span class="o">=</span><span class="w"> </span>swig_import_helper<span class="o">()</span>
<span class="w"> </span>File<span class="w"> </span><span class="s2">"/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py"</span>,<span class="w"> </span>line<span class="w"> </span><span class="m">24</span>,<span class="w"> </span><span class="k">in</span><span class="w"> </span>swig_import_helper
<span class="w"> </span><span class="nv">_mod</span><span class="w"> </span><span class="o">=</span><span class="w"> </span>imp.load_module<span class="o">(</span><span class="s1">'_adfrcc'</span>,<span class="w"> </span>fp,<span class="w"> </span>pathname,<span class="w"> </span>description<span class="o">)</span>
ImportError:<span class="w"> </span>dlopen<span class="o">(</span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so,<span class="w"> </span>0x0002<span class="o">)</span>:<span class="w"> </span>Library<span class="w"> </span>not<span class="w"> </span>loaded:<span class="w"> </span>/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib
<span class="w"> </span>Referenced<span class="w"> </span>from:<span class="w"> </span><424BF61E-BF0F-351E-B546-E82EBBD8FBF5><span class="w"> </span>/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so
<span class="w"> </span>Reason:<span class="w"> </span>tried:<span class="w"> </span><span class="s1">'/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/local/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file<span class="o">)</span>,<span class="w"> </span><span class="s1">'/usr/lib/libgomp.1.dylib'</span><span class="w"> </span><span class="o">(</span>no<span class="w"> </span>such<span class="w"> </span>file,<span class="w"> </span>not<span class="w"> </span><span class="k">in</span><span class="w"> </span>dyld<span class="w"> </span>cache<span class="o">)</span>
➜<span class="w"> </span>3Q47
</code></pre>
</div>
<p>Sometimes this error is simply outputted as a segmentation fault. But, it is because it cannot find the <code>libgomp.1.dylib</code>. I haven't tested using a newer version of GCC to make it work. Building GCC 8 yourself is absolutely painful. We are going to use a copy generated by the homebrew team.</p>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>../../
$<span class="w"> </span><span class="nb">pwd</span>
/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0
$<span class="w"> </span>curl<span class="w"> </span>-L<span class="w"> </span>-H<span class="w"> </span><span class="s2">"Authorization: Bearer QQ=="</span><span class="w"> </span>-o<span class="w"> </span>gcc8amd64.tar.gz<span class="w"> </span>https://ghcr.io/v2/homebrew/core/gcc/8/blobs/sha256:438d5902e5f21a5e8acb5920f1f5684ecfe0c645247d46c8d44c2bbe435966b2
$<span class="w"> </span>tar<span class="w"> </span>-xzf<span class="w"> </span>gcc8amd64.tar.gz
$<span class="w"> </span>cp<span class="w"> </span>-r<span class="w"> </span>gcc@8/8.5.0/lib/gcc/8/*<span class="w"> </span>clean_install/lib/
</code></pre>
</div>
<p>Now, we should be able to go back and run the target generation command:</p>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span><span class="nb">cd</span><span class="w"> </span>ADCP_tutorial_data/3Q47
$<span class="w"> </span>agfr<span class="w"> </span>-r<span class="w"> </span>3Q47_recH.pdbqt<span class="w"> </span>-l<span class="w"> </span>3Q47_pepH.pdbqt<span class="w"> </span>-asv<span class="w"> </span><span class="m">1</span>.1<span class="w"> </span>-o<span class="w"> </span>3Q47
<span class="c1">#################################################################</span>
<span class="c1"># If you used AGFR in your work, please cite: #</span>
<span class="c1"># #</span>
<span class="c1"># P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and #</span>
<span class="c1"># M.F. Sanner #</span>
<span class="c1"># AutoDockFR: Advances in Protein-Ligand Docking with #</span>
...
</code></pre>
</div>
<h3 id="docking-peptide">Docking Peptide</h3>
<div class="codehilite">
<pre><span></span><code>$<span class="w"> </span>adcp<span class="w"> </span>-t<span class="w"> </span>3Q47.trg<span class="w"> </span>-s<span class="w"> </span>npisdvd<span class="w"> </span>-N<span class="w"> </span><span class="m">20</span><span class="w"> </span>-n<span class="w"> </span><span class="m">1000000</span><span class="w"> </span>-o<span class="w"> </span>3Q47_redocking<span class="w"> </span>-ref<span class="w"> </span>3Q47_pepH.pdb
</code></pre>
</div>
<p>There you have it. Running ADCP on the newest macOS version against all odds.</p>
<p>I haven't yet looked into fixing/patching <code>agfrgui</code> as I don't use the software. But, if someone reallllly needs to run it on Apple Silicon, I am happy to take a look at monkeypatching it.</p>
<p>In case years down the line the prebuilt version of GCC 8 is not available, let me know so I can replace the link with my mirror.</p>
</div>
<blockquote>If you have scrolled this far, consider subscribing to my mailing list <a href="https://listmonk.navan.dev/subscription/form">here.</a> You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.</blockquote>
<script data-isso="https://comments.navan.dev/"
src="https://comments.navan.dev/js/embed.min.js"></script>
<section id="isso-thread">
<noscript>Javascript needs to be activated to view comments.</noscript>
</section>
</div>
<script src="assets/manup.min.js"></script>
<script src="/pwabuilder-sw-register.js"></script>
</body>
</html>
|
