<p style="margin-bottom: 0cm; margin-top: 0pt;">Dear all,</p>
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</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">Firstly, I wish you a happy new year filled with joy, health and lots of finding !!<br>
</p>
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</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">Now my question: </p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">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.</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"> </p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">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. </p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">I used the following command for the two systems </p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">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</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">I choose the option 2 (Protein-H) in the menu. It is the correct combination for g_sas ?</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"> </p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"> </p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
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)<br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">---- System A</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">@ s0 legend "Average (nm\S2\N)"<br>
@ s1 legend "Standard deviation (nm\S2\N)"<br>
545 0.723556 0.0709648<br>
546 0.851864 0.0780804<br>
547 0.782327 0.0548426<br>
548 0.97012 0.0836672<br>
549 0.339449 0.0611941<br>
550 0.839293 0.0795415<br>
551 1.34999 0.104301<br>
552 0.708079 0.0693484<br>
553 1.95306 0.135732<br>
554 1.02126 0.0899936<br>
555 0.32233 0.0755605<br>
556 0.643128 0.0645317<br>
557 0.842983 0.0683777<br>
558 1.37868 0.107237<br>
559 0.972423 0.108448<br>
560 0.875918 0.0707144<br>
561 0.56353 0.0494754<br>
562 0.979795 0.0875196<br>
563 0.6764 0.0599796<br>
564 0.792996 0.0830322<br>
565 1.29532 0.123898<br>
566 0.493239 0.0679436<br>
567 0.991596 0.0743836<br>
568 1.71456 0.121319<br>
569 0.943561 0.0747361<br>
570 1.12007 0.0511916<br>
571 0.572433 0.0343254<br>
<br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">---- System B <br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">@ s0 legend "Average (nm\S2\N)"<br>
@ s1 legend "Standard deviation (nm\S2\N)"<br>
545 0.721979 0.0582663<br>
546 0.905305 0.0508979<br>
547 0.785995 0.053198<br>
548 0.944034 0.0688671<br>
549 0.394531 0.0606229<br>
550 0.803279 0.0667054<br>
551 1.38402 0.083296<br>
552 0.920283 0.06624<br>
553 1.824 0.127784<br>
554 0.688272 0.0821362<br>
555 0.50046 0.0694137<br>
556 0.870991 0.0733946<br>
557 0.765114 0.0651865<br>
558 1.27511 0.116357<br>
559 1.14207 0.0791716<br>
560 0.950344 0.0677436<br>
561 0.564978 0.052539<br>
562 0.983167 0.0857281<br>
563 0.670499 0.0607886<br>
564 0.814746 0.0638795<br>
565 1.16659 0.0778935<br>
566 0.551229 0.0534253<br>
567 1.02231 0.0561598<br>
568 1.69817 0.115372<br>
569 0.878103 0.0621447<br>
570 0.982666 0.0652861<br>
571 0.742895 0.0373423</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">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 ?<br>
</p>
<br>
<p style="margin-bottom: 0cm; margin-top: 0pt;">Thank you in advance for your help/advices. </p>
<p style="margin-bottom: 0cm; margin-top: 0pt;"><br>
</p>
<p style="margin-bottom: 0cm; margin-top: 0pt;">Stephane<br>
</p>