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)
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Received on Tue Jun 04 2013 - 13:30:03 PDT
