sa wrote:
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 ?
No. If you have a DPC micelle, it needs to be part of the calculation group, as
well. The output group can then be whatever you want it to be. But if you
don't consider the micelle, g_sas will happily calculate SASA as if your peptide
were simply in water. Your results seem to agree.
g_sas -h:
..."The calculation group should always consists of all the non-solvent atoms in
the system"...
-Justin
Thank you in advance for your help/advices.
Stephane
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
