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
>>
>
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Received on Tue Jun 04 2013 - 13:30:02 PDT
