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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Received on Tue Jun 04 2013 - 10:00:02 PDT
