VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Tue May 03 2011 - 09:34:57 CDT

Hi Jesper,

I ran into a similar problem trying to calculate the SASA of the hydrophobic
chains of a lipid bilayer. The SASA calculator includes the chain surface
around the boudary, which are obviously hidden by periodic images. So (at
the suggestion of Axel K if I remember correctly) I replicated the system
periodically at the edges of the bilayer, then wrote a new system which
includes the periodic images. Then I used the -restrict option for sasa to
include only the original periodic cell.

hth,
E

2011/5/3 Jesper Sørensen <lists_at_jsx.dk>

> Hi Alex,
>
> Thanks for the suggestions and clarifying the problems.
> I can see there are a lot of issues to deal with. I'll try to think,
> whether
> there is a better way to express the information that I want from the
> simulations.
>
> Best regards,
> Jesper
>
> -----Original Message-----
> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> Sent: 3. maj 2011 15:32
> To: Jesper Sørensen
> Subject: Re: vmd-l: SASA calculation using periodic images?
>
> jesper,
>
> please always cc: the list when replying. thanks.
>
> 2011/5/3 Jesper Sørensen <lists_at_jsx.dk>:
> > Hi Alex,
> >
> > Thanks for the reply. Sorry about pasting the wrong old-post in. It
> > was an old message from John Stone, who hinted that he would perhaps
> > make some changes to the code to handle these periodic images in SASA
> calculations.
> >
> > Perhaps you can tell me if I understand this correctly.
> > SASA is defined in AtomSel.py, which means the calculation is tied in
> > with
>
> AtomSel.py is just a wrapper for the internal VMD code.
>
> > the way selections in vmd is handled. Since there is no way (that I
> > know of) to select atoms in the periodic images without also selecting
> > them in the "original" image, that is where the problem arises to begin
> with?
>
> there are a number of issues here.
>
> - you have to identify and define individual clusters with PBC
> - you have to make the SASA calculations work with PBC
> - you have to figure out, whether the SASA is a good measure
> at all for clusters that are self-assembling. what about radius
> of gyration, for example?
> - you have to figure out a good way to summarize your results
> and hand it back the VMD script level.
>
> all of that requires some effort and this gets more complicated by the fact
> that VMD in its original conceptions assumes to be processing one huge
> protein immersed in a block of small water molecules and perhaps a few
> ions.
>
> > So, as you said, I will have to re-write the way atoms are selected in
> > vmd to be able to calculate what I am aiming for?
>
> i don't know exactly what you have to do. this is a complex problem and i
> am
> not even convinced that VMD is the best tool to do this unless you are
> comfortable hacking complex legacy c++ code.
> i would recommend before going full throttle to first perhaps construct a
> test system that has no PBC issues and test if the kind of analysis that
> you
> want to do will be giving you meaningful answers and try to see if there
> are
> alternate ways to get something equivalent more easily.
>
> cheers,
> axel.
>
> >
> > Best regards,
> > Jesper
> >
> > -----Original Message-----
> > From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> > Behalf Of Axel Kohlmeyer
> > Sent: 3. maj 2011 14:11
> > To: Jesper Sørensen
> > Cc: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: SASA calculation using periodic images?
> >
> > 2011/5/3 Jesper Sørensen <lists_at_jsx.dk>:
> >> Hello all,
> >>
> >>
> >>
> >> I want to calculate the solvent accessible surface area in a system
> >> with many monomers that aggregate. The aggregation occurs across the
> >> periodic images and therefore the wrapping of the system gets a
> >> little
> > complicated.
> >>
> >>
> >>
> >> Is there a way to make the SASA script/plugin in vmd take the
> >> periodic images into account when calculating the SASA of certain
> surfaces?
> >
> > no. at least not without significant modification of the VMD source code.
> >
> >>
> >> I found the below post on the VMD list from March of 2010, but I
> >> haven’t seen any changes to the SASA script since. Does anybody have
> >> an updated version that includes the periodic images?
> >
> > i don't understand. the quoted post is from yesterday and has nothing
> > to do with SASA.
> >
> >> I am more than willing to make the code change myself – but I am not
> >> sure how complicated it would be…
> >
> > anything with PBC inside VMD is somewhat complicated.
> >
> > cheers,
> > axel.
> >
> >
> > From: John Stone (johns_at_ks.uiuc.edu)
> > Date: Thu Mar 04 2010 - 10:50:11 CST
> > Next message: Filippo Federici: "Re: CUDA issues"
> > Previous message: John Stone: "Re: CUDA issues"
> > In reply to: Edward Lyman: "Re: 2 questions about "measure sasa""
> > Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [
> > attachment ]
> >
> > Hi,
> > If you're getting surface area due to periodic boundaries, the
> > easiest solution (at present) would be to replicate the structure
> > across the boundary before doing the calculation, or use the PBC tools
> > plugins to unwrap the parts of the structure crossing the boundary. I
> > hope to implement
> >
> > handling of periodic cells in the SASA calculation, but it I haven't
> > started
> >
> > working on it yet.
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Fri, Feb 26, 2010 at 12:44:59PM -0700, Edward Lyman wrote:
> >> Hi again,
> >>
> >> The -restrict option is working very well, except that I have
> >> contributions coming from the boundaries of the box that the sasa
> >> algorithm thinks are exposed to the solvent. Is there some simple way
> >> to eliminate those contributions? The only way that comes to mind is
> >> to include an extra layer of lipids around the edges from the
> >> periodic image,
> >
> >> and then use restrict to eliminate that layer. maybe there is a
> >> clever atom selection taht will do the trick...
> >>
> >> any ideas are greatly appreciated!
> >>
> >> Ed
> >>
> >> On Thu, Feb 25, 2010 at 4:00 PM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
> >>
> >> Hi,
> >> Sorry for being slow to reply, I've been swamped finishing papers and
> >> getting some new code up and running...
> >>
> >> For 1) you would feed the list of points into 'draw' commands to draw
> >> them however you like.
> >>
> >> For 2) yes, the -restrict command can be used to prevent part of the
> >> structure from contributing. You can visualize the points to help you
> >> figure that out.
> >>
> >> Let us know if you need more help.
> >>
> >> Cheers,
> >> John Stone
> >> vmd_at_ks.uiuc.edu
> >> On Wed, Feb 17, 2010 at 01:40:53PM -0700, Edward Lyman wrote:
> >> > Hi all,
> >> >
> >> > 2 questions about vmd's built in sasa calculator:
> >> >
> >> > (1) how do i visualize the surface data after i store it using the
> >> -points
> >> > option?
> >> > (2) will the following command measure for me the sasa for $subsel,
> >> > excluding the surface area of $subsel that is occluded by $sel?
> >> >
> >> > measure sasa [atomselect top "$sel"] -restrict [atomselect top
> >> "$subsel"]
> >> >
> >> > Thanks!
> >> > Ed
> >>
> >> --
> >> NIH Resource for Macromolecular Modeling and Bioinformatics Beckman
> >> Institute for Advanced Science and Technology University of Illinois,
> >> 405 N. Mathews Ave, Urbana, IL 61801
> >> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> >> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics Beckman
> > Institute for Advanced Science and Technology University of Illinois,
> > 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science Temple University,
> Philadelphia PA, USA.
>
>
>