Hi Dan,
Yes, you were right (of course). I used AmberTools from someone else to
quickly test it, but although he'd updated the code, he didn't recompile.
Upgraded to AmberTools 13 / cpptraj 13.1 myself now, and all is fine.
Thanks!
Marc
On 4 June 2013 22:01, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Based on the files you gave me I don't think you were using cpptraj
> from AmberTools 13. Here's the cpptraj input I used:
>
> parm strip.prmtop
> trajin test.nc
> surf out TEMP.dat
>
> Here's my output for version 13.0 (there are some bugfixes after this
> one but the output is the same):
>
> CPPTRAJ: Trajectory Analysis. V13.0
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> INPUT: Reading Input from file surf.in
> ...
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM [strip.prmtop] (1 actions):
> 0: [surf out TEMP.dat]
> SURF: 7438 solute atoms.
> LCPO surface area will be calculated for 7438 atoms.
> ----- [test.nc] (1-1, 1) -----
> 100% Complete.
>
> Read 1 frames and processed 1 frames.
> ...
>
> I do get the error you saw using the same input with version 12.5 of
> cpptraj:
>
> CPPTRAJ: Trajectory Analysis. V12.5
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from file surf.in
> ...
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> PARM [strip.prmtop]: Setting up 1 actions.
> 0: [surf out TEMP.dat]
> [strip.prmtop] Setting surface parameters for -1733393274 solute atoms.
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
> Aborted (core dumped)
>
> Check that you're using the correct binary ('cpptraj --version' will
> show the version number), and if so make sure it passes all tests.
>
> -Dan
>
> On Tue, Jun 4, 2013 at 2:12 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> > Hi,
> >
> > Can you send me off-list the topology and 1 frame of the coordinates
> > that give you this behavior? Thanks.
> >
> > -Dan
> >
> > On Tue, Jun 4, 2013 at 2:10 PM, Marc van der Kamp
> > <marcvanderkamp.gmail.com> wrote:
> >> Hi again,
> >>
> >> Sorry, my version was actually AmberTools12 up to bugfix.36.
> >> AmberTools 13.00 gives the same error.
> >>
> >> Would updating to AmberTools 13.7 make a difference? (From the
> description
> >> of the updates, it doesn't look like it)
> >> I'll try it, but that may have to wait till Thursday.
> >>
> >> --Marc
> >>
> >>
> >> On 4 June 2013 19:38, Marc van der Kamp <marcvanderkamp.gmail.com>
> wrote:
> >>
> >>> Hi Dan,
> >>>
> >>> AmberTools12, I think up to bugfix 18 or so.
> >>> I can try with v13.
> >>>
> >>> Marc
> >>> On Jun 4, 2013 7:04 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> What version of cpptraj are you using?
> >>>>
> >>>> -Dan
> >>>>
> >>>> On Tue, Jun 4, 2013 at 10:32 AM, Marc van der Kamp
> >>>> <marcvanderkamp.gmail.com> wrote:
> >>>> > Hi,
> >>>> >
> >>>> > I was hoping to run 'surf' (calculate solvent accessible surface
> area
> >>>> with
> >>>> > LCPO algorithm), using trajectory files stripped from solvent
> previously
> >>>> > written by cpptraj as input.
> >>>> > Unfortunately, this doesn't seem to work - cpptraj 'crashes' once it
> >>>> tries
> >>>> > to process the trajectory.
> >>>> > I get the following error:
> >>>> >
> >>>> > terminate called after throwing an instance of 'std::bad_alloc'
> >>>> > what(): std::bad_alloc
> >>>> >
> >>>> > And this is the last line from the output:
> >>>> > [strip.prmtop] Setting surface parameters for -772450410 solute
> atoms.
> >>>> >
> >>>> > The input-script I use does work for the full trajectories
> (including
> >>>> > solvent), in which case the equivalent line makes sense (i.e. lists
> >>>> total
> >>>> > solute atoms)
> >>>> > [full.prmtop] Setting surface parameters for 7443 solute atoms.
> >>>> >
> >>>> > Is this due to the way the algorithm is implemented, or is something
> >>>> else
> >>>> > going on? Might there be a way around it?
> >>>> > (The reason I want to use a trajectory without solvent is that my
> >>>> complete
> >>>> > trajectory is stored on a disk that I don't have access to from
> compute
> >>>> > nodes. I do of course use a prmtop for the stripped trajectory,
> which
> >>>> works
> >>>> > fine for other analyses such as distance.)
> >>>> >
> >>>> > Thanks in advance,
> >>>> > Marc
> >>>> > _______________________________________________
> >>>> > AMBER mailing list
> >>>> > AMBER.ambermd.org
> >>>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>>
> >>>>
> >>>> --
> >>>> -------------------------
> >>>> Daniel R. Roe, PhD
> >>>> Department of Medicinal Chemistry
> >>>> University of Utah
> >>>> 30 South 2000 East, Room 201
> >>>> Salt Lake City, UT 84112-5820
> >>>> http://home.chpc.utah.edu/~cheatham/
> >>>> (801) 587-9652
> >>>> (801) 585-9119 (Fax)
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-9119 (Fax)
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jun 05 2013 - 14:30:03 PDT
