I can't tell what might be happening from the information you've
provided. Can you paste or attach the full output from cpptraj,
including any error messages (i.e. stdout + stderr).
-Dan
On Thu, Sep 14, 2017 at 11:33 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Further to my last message I forgot to include the following cpptraj output
>
> DATAFILES (2 total):
> sum.out (Standard Data File): SPAM_00001[DG] SPAM_00001[DH] SPAM_00001[-TDS]
> spam.info (SPAM info)
> Warning: Set 'SPAM_00001[DG]' contains no data.
> Warning: Set 'SPAM_00001[DH]' contains no data.
> Warning: Set 'SPAM_00001[-TDS]' contains no data.
> Warning: File 'sum.out' has no sets containing data.
>> On 14 Sep 2017, at 18:30, George Tzotzos <gtzotzos.me.com> wrote:
>>
>> Thank you Dan,
>>
>> I modified my input file by removing the [purewater] option
>>
>> spam mypeakfile.xyz solv WAT reorder cut 12 summary sum.out dgbulk -30.3 dhbulk -22.2 temperature 300
>>
>> cpptraj produced spam.info <http://spam.info/> but not the sum.out file.
>>
>> Is there something I’m missing?
>>
>> Many thanks
>>
>> George
>>
>>> On 14 Sep 2017, at 18:16, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> For the SPAM 'purewater' option you only need specify data set name,
>>> cutoff, and output file 'out <file>' since all you are doing is
>>> calculating bulk values.
>>>
>>> -Dan
>>>
>>> On Thu, Sep 14, 2017 at 11:13 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>>> Trying to run SPAM
>>>>
>>>> spam mypeakfile.xyz solv WAT reorder purewater cut 12 summary sum.out dgbulk -30.3 dhbulk -22.2 temperature 300
>>>>
>>>> cpptraj throws the error:
>>>>
>>>> INPUT: Reading input from 'spam.in'
>>>> [parm subA_solv.prmtop]
>>>> Reading 'subA_solv.prmtop' as Amber Topology
>>>> Radius Set: H(N)-modified Bondi radii (mbondi2)
>>>> [trajin prod_100ns.nc]
>>>> Reading 'prod_100ns.nc' as Amber NetCDF
>>>> [spam mypeakfile.xyz solv WAT reorder purewater cut 12 summary sum.out dgbulk -30.3 dhbulk -22.2 temperature 300]
>>>> SPAM:
>>>> Calculating bulk value for pure solvent
>>>> Using a 12.00 Angstrom non-bonded cutoff with shifted EEL.
>>>>
>>>> Error: [spam] Not all arguments handled: [ mypeakfile.xyz reorder summary sum.out dgbulk -30.3 dhbulk -22.2 temperature 300 ]
>>>> 1 errors encountered reading input.
>>>> TIME: Total execution time: 0.0665 seconds.
>>>> Error: Error(s) occurred during execution.
>>>>
>>>> The head of the peaks.xyz file generated with volmap is:
>>>> 727
>>>>
>>>> C 3.46464014 25.54114723 39.11305046 0.03241467
>>>> C 3.46464014 26.54114723 40.11305046 0.03353754
>>>> C 3.46464014 28.54114723 40.11305046 0.03223133
>>>> C 3.46464014 29.04114723 37.61305046 0.03259914
>>>> C 3.46464014 30.04114723 41.11305046 0.03254872
>>>> C 3.46464014 31.54114723 28.11305046 0.03995054
>>>> C 3.46464014 32.04114723 38.11305046 0.02878203
>>>> C 3.46464014 33.04114723 42.61305046 0.02801451
>>>>
>>>> Any help would be much appreciated
>>>>
>>>> Regards
>>>>
>>>> George
>>>>
>>>> _______________________________________________
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>>>> 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
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
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>
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> 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 Thu Sep 14 2017 - 09:00:05 PDT
