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
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Received on Mon Dec 11 2017 - 09:00:02 PST
