[gmx-users] any alternative methods?

[Justin Lemkul]

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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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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