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
--
-------------------------
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 - 08:00:03 PST
