The ambmask syntax is quite robust albeit arguably less "natural" than
VMD's syntax. Nonetheless it is equally as powerful in all situations I
have encountered. I think there are some slight "gotchas" with distance
based cutoffs, but that's it.
It is also well described in the manual, although I forget if it is in the
Amber or AmberTools version.
Regards,
Brian
On Fri, May 16, 2014 at 12:40 PM, Ben Ahmady <ahmady.ben.gmail.com> wrote:
> Hi Brian,
>
> Thanks for your reply. I can only assume that the reference sites are
> indeed near the boundary, which explains the discrepancies I'm seeing. I
> think I've managed to make sense of cpptraj's radial function and getting
> it to recognise my truncated octahedron and PBC correctly, but I'm having
> trouble getting VMD to give me numbers of sodium ions within certain
> regions/distances of sulphur atoms (in the surfactant) because I believe
> that it too is getting conflicting information somewhere. That was why I
> saved my "image familiar" (via ptraj) centred coordinates in NETCDF,
> because I was getting the "diamond shaped holes" (which I read about here:
> http://archive.ambermd.org/201006/0595.html) in other formats. The problem
> is "pbc box" just gives me something orthorhombic so yes, I think you're
> right that VMD can only handle those.
>
> Is there any way I can determine the number of atoms/ions of a particular
> mask within a region of another mask, (a la "$sel num" in VMD, after
> setting "sel" to something like "'X' and within Y of name 'Z'")? Or will I
> just have to re-run my coordinates with a solvated box rather than
> truncated octahedron?
>
>
> Many thanks in advance,
>
> Ben
>
>
> On 16 May 2014 15:45, Brian Radak <radak004.umn.edu> wrote:
>
> > Without accounting for PBCs RDFs are definitely sensitive to wrapping if
> > the reference sites are near the boundary. This sounds like it might be
> the
> > case for you if you don't just have a single macromolecule in the center
> of
> > a water box. Cpptraj can definitely solve this problem by handling PBCs
> > correctly when doing the RDF calculation (see the "radial" function in
> the
> > AmberTools manual). The RDF utility in VMD, on the other hand, can only
> > handle orthorhombic conditions (to the best of my knowledge), although it
> > will not tell you that it has messed up the coordinates.
> >
> > Regards,
> > Brian
> >
> > P.S. There is no real gain in converting an ASCII trajectory to NetCDF
> > format after the fact except to compress the data and speed up file
> > reading; all of the precision is already lost. I would recommend ALWAYS
> > using ioutfm = 1 and ntxo = 2 whenever running AMBER.
> >
> >
> > On Fri, May 16, 2014 at 10:29 AM, Ben Ahmady <ahmady.ben.gmail.com>
> wrote:
> >
> > > Dear AMBER Users & Developers,
> > >
> > > I've developed an SDS micelle trajectory in AMBER of 60 surfactants,
> and
> > > I've taken a window of the last 4ns of a ~25ns NPT run with iwrap=0,
> > using
> > > ptraj, and put it into a NETCDF-formatted coordinate file, using the
> > > commands:
> > >
> > > """
> > > trajin last4ns.crd
> > > center :1-60
> > > image familiar
> > > trajout centre.crd netcdf
> > > """
> > >
> > > I've then generated an RDF with the following command:
> > >
> > > """
> > > radial centre 0.1 10 :1-60.S39 :61-120 :SDS.S39 density 0.00088
> noimage
> > > """
> > >
> > > This gives me something sensible looking, with coordination shells I'd
> > > expect from previous work, but I've gotten very confused about how I
> > should
> > > go about "counting" the number of ions within distances corresponding
> to
> > > the coordination shell boundaries. The only way I can think of is to
> use
> > > VMD commands of the order:
> > >
> > > """
> > > set sel [atomselect top "all name 'Na+' and within X of name 'S39'"]
> > > $sel num
> > > """
> > >
> > > ... but I'm not sure if I should be using wrapped coordinates, or an
> > > average structure (via ptraj's "average" routine), or whether I should
> be
> > > including imaging, and so on. I get different results for different
> > > combinations I've tried — so to put it another way I don't know which
> one
> > > is actually giving me the "right" answer.
> > >
> > > Apologies if this would be better suited to the VMD mailing list, but I
> > > thought it might have more to do with the way I've generated my
> > > coordinates, implying I actually need help with AMBER/ptraj. In any
> case,
> > > any assistance would be greatly appreciated.
> > >
> > >
> > > Best regards,
> > >
> > > Ben Ahmady
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Center for
> Integrative
> > Proteomics Room 308
> > Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Ben Ahmady
>
> Molecular Modelling & Materials Science (M3S) Centre
> Department of Chemistry
> University College London
> http://www.m3s.ucl.ac.uk/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
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Received on Fri May 16 2014 - 11:00:02 PDT
