[gmx-users] g_sas values for peptide in water and in DPC micelle

[sa]

Dear all,


 Firstly, I wish you a happy new year filled with joy, health and lots of
finding !!


 Now my question:


 I have simulated one peptide (25 AA length + N- and C- caps) in two
environment: one in bulk water TIP3P water (A) and one with a DPC micelle in
water (B). My peptide keep in the two simulations a very similar secondary
structure (alpha helix). The peptide in the system B, during the last 50 ns
of the simulation time, is located in the micelle/water interface in the
little crevice formed by the DPC hydrophobic chain and remains in the same
place.

 I would like to compute the accessible surface area with respect to solvent
for some residues of the peptide and especially for the single TRP  of the
peptide (TRP553) and compare with the SA obtained for the same peptide in
water.  By examining several configurations of the peptide in the B system
at the end of the simulation (~150 ns) with pymol, I found that TRP553
residue is mainly in contact with the DPC micelle hydrophobic core and is
not fully exposed to the solvent. So i expect that the average SA value for
TRP553 (and for the others residues) in system B will be smaller than the
values obtained for the same residues in the system A.



 I used the following command for the two systems


 g_sas_mpi -f *.xtc -s md_0_24.tpr -b 99500 -e 100000 -dt 10 -or
mTM10-TIP3_per_residu_TRP553_SAS.xvg -oa mTM10-TIP3_per_atom_TRP553_SAS.xvg
-n System_TRP553.ndx


 I choose the option 2 (Protein-H) in the menu. It is the correct
combination for g_sas ?


The output of g_sas (gmx 4.5.3) are shown below for the two systems. Average
values are computed for A and B from the last  500 ps (extracted every 10
frames -> 50 values)


 ---- System A


 @ s0 legend "Average (nm\S2\N)"
@ s1 legend "Standard deviation (nm\S2\N)"
       545    0.723556  0.0709648
       546    0.851864  0.0780804
       547    0.782327  0.0548426
       548     0.97012  0.0836672
       549    0.339449  0.0611941
       550    0.839293  0.0795415
       551     1.34999   0.104301
       552    0.708079  0.0693484
       553     1.95306   0.135732
       554     1.02126  0.0899936
       555     0.32233  0.0755605
       556    0.643128  0.0645317
       557    0.842983  0.0683777
       558     1.37868   0.107237
       559    0.972423   0.108448
       560    0.875918  0.0707144
       561     0.56353  0.0494754
       562    0.979795  0.0875196
       563      0.6764  0.0599796
       564    0.792996  0.0830322
       565     1.29532   0.123898
       566    0.493239  0.0679436
       567    0.991596  0.0743836
       568     1.71456   0.121319
       569    0.943561  0.0747361
       570     1.12007  0.0511916
       571    0.572433  0.0343254

 ---- System B


 @ s0 legend "Average (nm\S2\N)"
@ s1 legend "Standard deviation (nm\S2\N)"
       545    0.721979  0.0582663
       546    0.905305  0.0508979
       547    0.785995   0.053198
       548    0.944034  0.0688671
       549    0.394531  0.0606229
       550    0.803279  0.0667054
       551     1.38402   0.083296
       552    0.920283    0.06624
       553       1.824   0.127784
       554    0.688272  0.0821362
       555     0.50046  0.0694137
       556    0.870991  0.0733946
       557    0.765114  0.0651865
       558     1.27511   0.116357
       559     1.14207  0.0791716
       560    0.950344  0.0677436
       561    0.564978   0.052539
       562    0.983167  0.0857281
       563    0.670499  0.0607886
       564    0.814746  0.0638795
       565     1.16659  0.0778935
       566    0.551229  0.0534253
       567     1.02231  0.0561598
       568     1.69817   0.115372
       569    0.878103  0.0621447
       570    0.982666  0.0652861
       571    0.742895  0.0373423


 As you can see, it is not the case since the SA values are not
significantly different between the two systems, i don t understand why. Did
i use use the good combination for g_sas ?

Thank you in advance for your help/advices.


 Stephane
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