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
> > _______________________________________________
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> > 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)
>
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>
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Received on Tue Jun 04 2013 - 12:00:02 PDT
