This message provides the clue to what is going on:
On Thu, Sep 14, 2017 at 12:04 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Not calculating any SPAM energies
Along with:
> Warning: No energies for 727 peaks.
I believe there is a minor bug in the code where the energy
calculation is only triggered if 'out' has been specified. Try adding
'out peakenergy.dat' or something similar to your command. I'll look
into the bug. Thanks for the report.
-Dan
>
> DATASETS (730 total):
> TEST:1 "TEST:1" (double), size is 0
> TEST:2 "TEST:2" (double), size is 0
> TEST:3 "TEST:3" (double), size is 0
> TEST:4 "TEST:4" (double), size is 0
> TEST:5 "TEST:5" (double), size is 0
> TEST:6 "TEST:6" (double), size is 0
> TEST:7 "TEST:7" (double), size is 0
> TEST:8 "TEST:8" (double), size is 0
> TEST:9 "TEST:9" (double), size is 0
> TEST:10 "TEST:10" (double), size is 0
> >>>>>>>>>>>>>>>>>>>>
> TEST:724 "TEST:724" (double), size is 0
> TEST:725 "TEST:725" (double), size is 0
> TEST:726 "TEST:726" (double), size is 0
> TEST:727 "TEST:727" (double), size is 0
> TEST[DG] "TEST[DG]" (X-Y mesh), size is 0
> TEST[DH] "TEST[DH]" (X-Y mesh), size is 0
> TEST[-TDS] "TEST[-TDS]" (X-Y mesh), size is 0
>
> DATAFILES (2 total):
> sum.out (Standard Data File): TEST[DG] TEST[DH] TEST[-TDS]
> spam.info (SPAM info)
> Warning: Set 'TEST[DG]' contains no data.
> Warning: Set 'TEST[DH]' contains no data.
> Warning: Set 'TEST[-TDS]' contains no data.
> Warning: File 'sum.out' has no sets containing data.
>
> RUN TIMING:
> TIME: Init : 0.0002 s ( 0.00%)
> TIME: Trajectory Process : 251.2216 s ( 99.42%)
> TIME: Action Post : 1.4516 s ( 0.57%)
> TIME: Analysis : 0.0000 s ( 0.00%)
> TIME: Data File Write : 0.0053 s ( 0.00%)
> TIME: Other : 0.0054 s ( 0.00%)
> TIME: Run Total 252.6841 s
> ---------- RUN END ---------------------------------------------------
> TIME: Total execution time: 252.7560 seconds.
>
> The spam.info <http://spam.info/> produced indicates that:
> # There are 727 density peaks and 10000 frames
>
>
>
>> On 14 Sep 2017, at 18:49, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>
>> 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
>>>>>
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>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
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>>
>>
>>
>> --
>> -------------------------
>> 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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>
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--
-------------------------
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 - 10:00:03 PDT
