From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Dec 15 2006 - 02:24:01 CST
Marcos, Peter and Cesar,
Thank you very much for your suggestions and for the script. After a
slight modification, it worked perfectly and got a system with no
water around the membrane. I also ran a couple of simulations and got
a much better system, with no membrane "crushing" at the edges and of
course no water around the hydrophobic region of the membrane. I
definitely will acknowledge you in the resulting paper! You helped me
to save a lot of time :)
Cheers,
Michel
2006/12/13, Marcos Sotomayor <sotomayo_at_ks.uiuc.edu>:
>
>
> No problem, the script should be something like this:
>
> package require solvate
> solvate yourprotein.psf yourprotein.pdb -o yourprotein_water_TEMP -b 1.5 -minmax {{-48 -48 -48} {48 48 48}}
> set all [atomselect top all]
> $all set beta 0
> set seltext "segid WT1 to WT99 and same residue as abs(z) <10"
> set sel [atomselect top $seltext]
> $sel set beta 1
> set badwater [atomselect top "name OH2 and beta > 0"]
> set seglist [$badwater get segid]
> set reslist [$badwater get resid]
> mol delete all
> package require psfgen
> readpsf kcsa_dppc_water_TEMP.psf
> coordpdb kcsa_dppc_water_TEMP.pdb
> foreach segid $seglist resid $reslist {
> delatom $segid $resid
> }
> writepdb yourproteinw.pdb
> writepsf yourproteinw.psf
> file delete yourprotein_water_TEMP.psf
> file delete yourprotein_water_TEMP.pdb
> exit
>
> - Note that solvate loads the resulting system so the command in the third
> line is working on yourportein_water_TEMP.
>
> - The key selection is in the fifth line, where we used segid's to avoid
> deleting other water molecules (crystallographic or others) and the abs(z)
> command permits you to delete water molecules on the hydrophobic region of
> your whole membrane. You will have to modify this selection to avoid
> selecting water molecules present in a channel, for off-center membranes,
> etc. Take into account that you want to keep water molecules in the
> hydrophilic regions of the membrane, don't include them in this selection!
>
> Hope it helps,
> Marcos
>
> On Wed, 13 Dec 2006, L. Michel Espinoza-Fonseca wrote:
>
> > This thing about a tcl script to remove such waters sounds good too.
> > Do you already have it available? It'll be nice if you could share it
> > with some of us :)
> >
> > Michel
> >
> > 2006/12/13, Marcos Sotomayor <sotomayo_at_ks.uiuc.edu>:
> >>
> >>
> >>
> >> On Wed, 13 Dec 2006, L. Michel Espinoza-Fonseca wrote:
> >>
> >> > Thank you for your comments.
> >> >
> >> > I think I wrote that I was measuring the size of the lipid bilayer,
> >> > but I was wrong. I'm indeed measuring the distance of the whole box
> >> > (water+lipid), but I wrote the opposite :).
> >>
> >> Michel, if you are measuring the size of the box with the minmax command
> >> of VMD, DO NOT include the lipids in your selection, as the outcome will
> >> give you a box that's bigger in the xy plan that what it really is and
> >> you will have a gap between periodic images that will be filled with water.
> >>
> >> >
> >> > About the answer, yes, I guessed this behavior is not right, specially
> >> > because I don't want to simulate "floating discs" (i.e., a
> >> > lipid-protein system fully surrounded by water). When I build my
> >> > original system it looks good -no waters are found at the edges. Right
> >> > now I'm re-equilibrating everything and hope to get the right results
> >> > this time.
> >>
> >> Check your periodic images with VMD first, you may save some time by
> >> setting a smaller box in the xy plane.
> >>
> >> >
> >> > Now that this topic was raised, I was wondering how to add more water
> >> > to your lipid-protein-water system with "solvate". Usually, when I do
> >> > the following:
> >> >
> >> > solvate mypsf.psf mypdb.pdb -o myoutput -b 3.5 +z 20 -z 20
> >> >
> >> > But I still get some water molecules in the edges. Maybe you have some
> >> > hints about how to avoid that!
> >>
> >> Peter's hint is quite good. You can also use the regular solvate over the
> >> whole system and then delete the water molecules at the edges using a tcl
> >> script. A tutorial on how to do this and how to simulate membrane proteins
> >> will be released soon.
> >>
> >> Marcos
> >>
> >> >
> >> > Michel
> >> >
> >> > 2006/12/13, Marcos Sotomayor <sotomayo_at_ks.uiuc.edu>:
> >> >>
> >> >> Cesar is likely right, and you can easily check if the size of your
> >> >> cell box is OK by showing the periodic images of your system in VMD (if
> >> >> the periodic cell info is not included in the dcd, use the vmd command
> >> >> "molinfo top set a xxx", where xxx is the value you set for size of the
> >> >> periodic cell in the x direction, same thing with b and c for y and z,
> >> >> respectively; then use the periodic tab in the graphical representations
> >> >> window to visualize periodic images).
> >> >>
> >> >> Just to answer your original questions, the behavior you are observing
> >> is
> >> >> not normal (unless you want to simulate a disc), and you should not
> >> >> observe water molecules going into the hydrophobic region of the
> >> membrane
> >> >> (not even at the edges). You should also check that your initial
> >> >> condition is right, i.e., you don't have water molecules already at the
> >> >> edges of your simulation cell at the level of the hydrophobic region of
> >> >> your membrane.
> >> >>
> >> >> Marcos
> >> >>
> >> >>
> >> >> On Wed, 13 Dec 2006, Cesar Luis Avila wrote:
> >> >>
> >> >> > Well, indeed taking minmax from lipid selection is a common mistake.
> >> You
> >> >> > should take minmax from water box. This is because of the periodic
> >> nature
> >> >> of
> >> >> > the box. When writing the coordinates for the system some of the
> >> lipids
> >> >> that
> >> >> > were split in the boundaries get wrapped together resulting in a wider
> >> >> box
> >> >> > for lipids than it really is. Since water molecules are smaller, they
> >> are
> >> >> not
> >> >> > affected that much.
> >> >> > Regards
> >> >> > Cesar
> >> >> >
> >> >> > L. Michel Espinoza-Fonseca escribió:
> >> >> >> Dear Peter and Cesar,
> >> >> >>
> >> >> >> Thank you for your answers.
> >> >> >>
> >> >> >> Peter: Yes, I'm using pressure controls, but instead of
> >> >> >> useConstantRatio I'm using useConstantArea... What do you think?
> >> Maybe
> >> >> >> I should modify this and see what I get. I don't think I'll be a
> >> >> >> problem, since my system is actually in the x-y plane.
> >> >> >>
> >> >> >> Cesar: I'm using the x-y dimensions of the lipid to assign the length
> >> >> >> of my periodic box, so I think the problem is not actually being
> >> >> >> caused by this. Thank you anyway for the reminder!
> >> >> >>
> >> >> >> Cheers,
> >> >> >> Michel
> >> >> >>
> >> >> >> 2006/12/13, Peter Freddolino <petefred_at_ks.uiuc.edu>:
> >> >> >>> Hi Michel,
> >> >> >>> are you using pressure controls? If so, you may want to try adding
> >> >> >>> useConstantRatio to keep your x and y cell dimensions identical to
> >> each
> >> >> >>> other (this assumes that your membrane is in the x-y plane, so you
> >> may
> >> >> >>> need to rotate your system).
> >> >> >>> Peter
> >> >> >>>
> >> >> >>> L. Michel Espinoza-Fonseca wrote:
> >> >> >>> > Hi people,
> >> >> >>> >
> >> >> >>> > I have been performing a few simulations of protein-membrane
> >> systems
> >> >> >>> > using a flexible cell and PBC. I used the "membrane" plugin to
> >> build
> >> >> >>> > the membranes. I subjected such membranes to minimization and
> >> >> >>> > equilibration for a period of 0.5 ns. I get a pretty good
> >> >> equilibrated
> >> >> >>> > slab, so no problem there. The "problem" (I really don't know if
> >> >> >>> > that's a problem) is that after continuing my simulation for about
> >> 10
> >> >> >>> > ns, the shape of the lipid bilayer looks more like a "disc" than a
> >> >> >>> > "box". Moreover, water molecules start to surround the Z-axis
> >> edges
> >> >> of
> >> >> >>> > the membrane. Now my question is, is that normal? According to
> >> what I
> >> >> >>> > believe, it is not. how can I avoid this?
> >> >> >>> > All comments are very appreciated.
> >> >> >>> >
> >> >> >>> > Thanks a lot!
> >> >> >>> > Michel
> >> >> >>>
> >> >> >>
> >> >> >
> >> >>
> >> >
> >>
> >
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:42:57 CST