hello Justin:
thanks for reply.
I've read both the paper and manual script. As indicated from the
output, I found the following line:
368 4.295 3.8840018217
I just wondering how could it possible fro residue 368 with a value of 3.88?
For the pure lipids/water case, my apology for this since I forgot to
change the box size values but the protein/lipids case is with correct
box size.
best
Albert
On 08/22/2012 02:02 PM, Justin Lemkul wrote:
On 8/22/12 3:16 AM, Albert wrote:
On 08/22/2012 08:23 AM, Mark Abraham wrote:
The authors use a 200x200 grid in their first published work with
this tool.
What makes you think 20 is enough? (And even if it is enough, you still
haven't demonstrated another calculation showing that the APL with the
embedded protein should be different.)
Mark
Dear Mark:
thanks for kind comments. I also enlarge the grid size to 200 for
my system.
And I get similar results. What need to mention is that I've got
around 160 aa
are beruied in lipids and I don't know why only the following few
were mentioned
in calculations.
I don't know what you mean by "only the following few." The protein
is given one area value, as shown in the output file. The remaining
lines correspond to lipid residues, with the resid corresponding to
each. Embedded protein residues do not factor into the APL
calculation as they are not part of the grid surface used for the
calculation. Please see our paper on GridMAT-MD and several of the
figures within that demonstrate how the algorithm is applied.
I will also echo something Mark said - how does any of this relate to
the previous claim that GridMAT-MD does not reproduce the APL of a
pure bilayer? You've changed the topic here so it's hard to judge what
the question is at this point. Your pure POPC membrane starts out
reasonably enough; if you stick a large protein into the membrane, the
structure likely changes and you're now comparing apples and oranges.
Your protein occupies about one-third of the total lateral area of
each leaflet, which may indicate that you do not have a membrane of
sufficient size to recover bulk lipid properties that one would expect
to see far away from the protein.
-Justin
Ave APL = 50.4388701869839 sq. Ang
protein 5.0 1580.671044407
Resid Z-value Area (sq. Ang.)
354 3.675 64.6156666701
355 3.725 50.2566296323
356 2.97 34.4852282957
357 4.028 52.4928731054
358 3.217 58.2600273255
359 3.821 22.362434731
360 3.669 30.4835294491
361 3.899 60.1431797239
362 3.271 72.3836703135
363 3.02 63.7917874958
364 3.027 40.016988466
365 3.406 67.087304193
366 3.349 41.9001408644
367 3.481 53.9052374042
368 4.295 3.8840018217
369 3.605 45.6664456612
370 3.467 55.5529957528
371 3.403 65.2041517946
372 3.353 51.4335998813
373 2.663 48.7265683086
374 3.269 58.6131184002
375 4.064 48.6088712837
376 3.7 51.1982058315
377 3.785 54.0229344291
378 3.22 49.6681445078
379 3.638 67.6757893175
380 4.003 37.3099568933
381 2.718 45.3133545865
382 4.265 20.3615853077
383 3.28 63.7917874958
384 3.753 59.3193005496
385 3.445 45.7841426861
386 2.451 51.786690956
387 4.336 44.4894754122
388 3.554 67.5580922926
389 2.911 40.2523825158
390 3.447 78.857006683
391 3.13 58.0246332757
392 3.593 56.0237838524
393 3.09 58.3777243504
394 3.55 51.5512969062
395 3.91 14.9475221623
396 4.104 49.5504474829
397 3.695 34.4852282957
398 3.758 63.4386964211
399 3.41 61.9086350974
400 3.706 46.1372337608
401 4.261 53.3167522797
402 3.364 48.7265683086
403 3.869 56.3768749271
404 2.983 58.7308154251
405 3.773 53.5521463295
406 3.364 52.3751760805
407 3.869 41.3116557399
408 2.896 60.4962707986
409 3.758 24.2455871294
410 3.412 51.5512969062
411 4.184 54.8468136034
412 3.146 61.4378469978
413 3.572 48.7265683086
414 3.294 52.7282671552
415 3.363 47.07880996
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