[gmx-users] Solvent Accessible Area with different Claculation Groups

[Justin A. Lemkul]

Quoting Benjamin Lindner <ben at benlabs.net>:

> Hi,
>
> let me add some information here to clarify the problem we're facing:
>
> >>> I was wondering if anyone has some insight on why the two sasa values are
> >>> not identical.
> >>>
> >>  From g_sas -h:
> >>
> >> "The calculation group should always consists of all the non-solvent atoms
> >> in the system. The output group can be the whole or part of the
> calculation
> >> group."
> >>
> >> So, setting the calculation group to only include "mol1" is simply
> >> incorrect usage of the program.
>
> Yes and no. We don't know whether the algorithm has any hidden
> assumptions, e.g. that all non-selected atoms are solvent molecules -
> that's why we are posting this.... maybe someone has intricate
> knowledge which might explain the odd result.
> @Justin, since you argued that the usage is incorrect: Can you answer why?
> As we understand it, the selection groups should identify the solvent
> atoms (by not selecting them) and identify  which atoms should
> contribute to the total surface area (running sum).
>

>From the help information quoted above, the calculation group should be all
non-solvent atoms.  So if you're only selecting "mol1" (which does not comprise
the entirety of non-solvent atoms) then you're not specifying the right
information.  The program then assumes that everything else (that wasn't
selected) is to be considered solvent.  Thus, if you have "mol1" and "mol2" in
pure water, then a group of mol1+mol2 must be the calculation group, and (per
the documentation), either of those molecules can be the output group.

-Justin

> > I'm not sure this is correct actually (although there has been a bug in the
> > program for a long time). But if you want to e.g. compute the occluded area
> > in a protein-protein interaction you  have to compute A+B-AB
> > where A is the area of just protein A, ignoring everything else and so on.
> > The fact the OP does not get the same area (did he use the same molecules?)
> > is probably just poor sampling. Just wait a couple of hundred nanoseconds
> > and see whether the distributions overlap.
>
> We didn't do any averaging. The results we get are by frame/timestep.
> In particular:
> case a) system group: A, output group: A
> case b) system group: AB, output group: A
>
> It is possible for case b) to produce higher numbers for SASA than
> case a) for the same frames.
> However, this defies our logic: How can an addition of steric atoms
> (molecule B) increase the total SASA of A?
> That's why we're puzzled.
>
> Cheers,
> Benjamin
>
>
> >
> >
> >> -Justin
> >>
> >>> I am attaching a figure displaying the calculations described above,
> >>> obtained by:
> >>> g_sas -f /traj-0-37 -s top.tpr   -n index-1-2.ndx -b 0 -e 100 -ndots 24
> >>>
> >>> Many thanks for your help,
> >>>
> >>> Loukas
> >>>
> >>> Loukas Petridis
> >>> Post-doctoral Research Fellow
> >>> Center for Molecular Biophysics, Oak Ridge National Laboratory
> >>> Building 6011, MS 6309, Oak Ridge, TN 37831
> >>> 865-576-2576 http://cmb.ornl.gov/people/lpk
> >>>
> >>> ------------------------------------------------------------------------
> >>>
> >>>
> >>> ------------------------------------------------------------------------
> >>>
> >>
> >
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the www interface
> > or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> >
> >
> > --
> > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> > 865-241-1537, ORNL PO BOX 2008 MS6309
> >
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



========================================

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

========================================