Hi,
Based on the files you gave me I don't think you were using cpptraj
from AmberTools 13. Here's the cpptraj input I used:
parm strip.prmtop
trajin test.nc
surf out TEMP.dat
Here's my output for version 13.0 (there are some bugfixes after this
one but the output is the same):
CPPTRAJ: Trajectory Analysis. V13.0
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file surf.in
...
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM [strip.prmtop] (1 actions):
0: [surf out TEMP.dat]
SURF: 7438 solute atoms.
LCPO surface area will be calculated for 7438 atoms.
----- [test.nc] (1-1, 1) -----
100% Complete.
Read 1 frames and processed 1 frames.
...
I do get the error you saw using the same input with version 12.5 of cpptraj:
CPPTRAJ: Trajectory Analysis. V12.5
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
INPUT: Reading Input from file surf.in
...
BEGIN TRAJECTORY PROCESSING:
.....................................................
PARM [strip.prmtop]: Setting up 1 actions.
0: [surf out TEMP.dat]
[strip.prmtop] Setting surface parameters for -1733393274 solute atoms.
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted (core dumped)
Check that you're using the correct binary ('cpptraj --version' will
show the version number), and if so make sure it passes all tests.
-Dan
On Tue, Jun 4, 2013 at 2:12 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
--
-------------------------
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
Received on Tue Jun 04 2013 - 14:30:03 PDT
