Also I note that in the output you posted it seems like cpptraj
doesn't actually segfault. Was there additional input that was making
it segfault before?
-Dan
On Mon, Dec 11, 2017 at 11:38 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> OK, I tried to reproduce your error as best I could using similar
> input and was not able to with a recent version of cpptraj, so I would
> try updating your version of cpptraj first. Let me know if that works
> for you.
>
> -Dan
>
> On Mon, Dec 11, 2017 at 11:07 AM, Andreas Tosstorff
> <andreas.tosstorff.cup.uni-muenchen.de> wrote:
>> Here goes the output. It's not reporting any error from what I can tell.
>> But it also does not seem to be reading any of the specified
>> trajectories other than the first...
>>
>>
>> CPPTRAJ: Trajectory Analysis. V16.12
>>
>> ___ ___ ___ ___
>> | \/ | \/ | \/ |
>> _|_/\_|_/\_|_/\_|_
>>
>> | Date/time: 12/11/17 17:05:28
>> | Available memory: 22.002 GB
>>
>> INPUT: Reading input from 'cpptraj.in'
>> [parm ../HYN.parm7]
>> Reading '../HYN.parm7' as Amber Topology
>> [ensemble remd01.mdcrd.01 trajnames
>> ../02/remd01.mdcrd.02,../03/remd01.mdcrd.03,../04/remd01.mdcrd.04,../05/remd01.mdcrd.05,../06/remd01.mdcrd.06,../07/remd01.mdcrd.07,../08/remd01.mdcrd.08,../09/remd01.mdcrd.09,../10/remd01.mdcrd.10,../11/remd01.mdcrd.11,../12/remd01.mdcrd.12,../13/remd01.mdcrd.13,../14/remd01.mdcrd.14,../15/remd01.mdcrd.15,../16/remd01.mdcrd.16,../17/remd01.mdcrd.17,../18/remd01.mdcrd.18,../19/remd01.mdcrd.19,../20/remd01.mdcrd.20,../21/remd01.mdcrd.21,../22/remd01.mdcrd.22,../23/remd01.mdcrd.23,../24/remd01.mdcrd.24,../25/remd01.mdcrd.25,../26/remd01.mdcrd.26,../27/remd01.mdcrd.27,../28/remd01.mdcrd.28,../29/remd01.mdcrd.29,../30/remd01.mdcrd.30,../31/remd01.mdcrd.31,../32/remd01.mdcrd.32,../33/remd01.mdcrd.33,../34/remd01.mdcrd.34,../35/remd01.mdcrd.35,../36/remd01.mdcrd.36,../37/remd01.mdcrd.37,../38/remd01.mdcrd.38,../39/remd01.mdcrd.39,../40/remd01.mdcrd.40,../41/remd01.mdcrd.41,../42/remd01.mdcrd.42,../43/remd01.mdcrd.43,../44/remd01.mdcrd.44,../45/remd01.mdcrd.45,../46/remd01.mdcrd.46,../47/remd01.mdcrd.47,../48/remd01.mdcrd.48,../49/remd01.mdcrd.49,../50/remd01.mdcrd.50,../51/remd01.mdcrd.51,../52/remd01.mdcrd.52,../53/remd01.mdcrd.53,../54/remd01.mdcrd.54,../55/remd01.mdcrd.55,../56/remd01.mdcrd.56,../57/remd01.mdcrd.57,../58/remd01.mdcrd.58,../59/remd01.mdcrd.59,../60/remd01.mdcrd.60,../61/remd01.mdcrd.61,../62/remd01.mdcrd.62,../63/remd01.mdcrd.63,../64/remd01.mdcrd.64]
>> Reading 'remd01.mdcrd.01' as Amber NetCDF
>> TIME: Total execution time: 2.0239 seconds.
>> --------------------------------------------------------------------------------
>> To cite CPPTRAJ use:
>> Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
>> Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
>> Theory Comput., 2013, 9 (7), pp 3084-3095.
>>
>>
>> On 12/11/2017 04:53 PM, Daniel Roe wrote:
>>> Hi,
>>>
>>> Try using a more up-to-date version of cpptraj, either from AmberTools
>>> 17 or from GitHub (https://github.com/Amber-MD/cpptraj).
>>>
>>> By complete input I just mean the entire script you are using - if
>>> it's just the two commands that you listed ('parm' and 'ensemble')
>>> that's fine. By complete output I mean all of stdout/stderr. Probably
>>> the easiest way to obtain this is to put your commands in a file like
>>> so:
>>>
>>> parm ../HYN.parm7
>>> ensemble remd01.mdcrd.01
>>> <other commands>
>>>
>>> then run cpptraj and redirect all output to a file, e.g.:
>>>
>>> cpptraj -i script.in > test.out 2>&1
>>>
>>> Let me know if you have more questions,
>>>
>>> -Dan
>>>
>>> On Mon, Dec 11, 2017 at 10:47 AM, Andreas Tosstorff
>>> <andreas.tosstorff.cup.uni-muenchen.de> wrote:
>>>> Hi Daniel,
>>>>
>>>>
>>>> thanks for your quick response.
>>>>
>>>> CPPTRAJ: Trajectory Analysis. V16.12
>>>>
>>>> What exactly do you mean by entire in/output? Do you need the
>>>> trajectories and parameter files?
>>>>
>>>> cpptraj.log:
>>>>
>>>> # 12/11/17 14:55:44
>>>> parm ../HYN.parm7
>>>> ensemble remd01.mdcrd.01
>>>> quit
>>>> # 12/11/17 15:55:24
>>>> quit
>>>> # 12/11/17 16:03:53
>>>> parm ../HYA.parm7
>>>> parm ../HYN.parm7
>>>> # 12/11/17 16:07:41
>>>> parm ../HYN.parm7
>>>>
>>>>
>>>> Kind regards,
>>>>
>>>> Andy
>>>>
>>>>
>>>> On 12/11/2017 04:41 PM, Daniel Roe wrote:
>>>>> Hi,
>>>>>
>>>>> Which version of cpptraj are you using? Also, if possible could you
>>>>> provide your entire cpptraj input and output? Thanks.
>>>>>
>>>>> -Dan
>>>>>
>>>>> On Mon, Dec 11, 2017 at 10:12 AM, Andreas Tosstorff
>>>>> <andreas.tosstorff.cup.uni-muenchen.de> wrote:
>>>>>> Hi all,
>>>>>>
>>>>>> I am trying to analyze an REMD run with cpptraj using the ensemble
>>>>>> command. My input looks like this:
>>>>>>
>>>>>> > parm ../HYN.parm7
>>>>>> Reading '../HYN.parm7' as Amber Topology
>>>>>> > ensemble remd01.mdcrd.01 trajnames
>>>>>> ../02/remd01.mdcrd.02,../03/remd01.mdcrd.03,../04/remd01.mdcrd.04,...,../64/remd01.mdcrd.64
>>>>>>
>>>>>> And the output like this:
>>>>>>
>>>>>> Reading 'remd01.mdcrd.01' as Amber NetCDF
>>>>>> Segmentation fault
>>>>>>
>>>>>> After that, cpptraj just closes.
>>>>>>
>>>>>> I am not too familiar with cpptraj and how to troubleshoot, so I'd
>>>>>> really appreciate your advice! PLease let me know if you need any
>>>>>> additional info.
>>>>>>
>>>>>> Kind regards,
>>>>>> Andreas
>>>>>>
>>>>>>
>>>>>> --
>>>>>> M.Sc. Andreas Tosstorff
>>>>>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
>>>>>> Department Pharmazie
>>>>>> LMU München
>>>>>> Butenandtstr. 5-13 ( Haus B)
>>>>>> 81377 München
>>>>>> Germany
>>>>>> Tel.: +49 89 2180 77059
>>>>>>
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>> --
>>>>
>>>>
>>>> --
>>>> M.Sc. Andreas Tosstorff
>>>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
>>>> Department Pharmazie
>>>> LMU München
>>>> Butenandtstr. 5-13 ( Haus B)
>>>> 81377 München
>>>> Germany
>>>> Tel.: +49 89 2180 77059
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>> --
>>
>>
>> --
>> M.Sc. Andreas Tosstorff
>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
>> Department Pharmazie
>> LMU München
>> Butenandtstr. 5-13 ( Haus B)
>> 81377 München
>> Germany
>> Tel.: +49 89 2180 77059
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Dec 11 2017 - 09:00:04 PST
