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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--
-------------------------
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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Received on Tue Jun 04 2013 - 11:30:02 PDT
