Thank you Dan,
I’ve modified the spam.in file as follows:
spam mypeakfile.xyz solv WAT reorder name TEST cut 12 summary sum.out out mydata.dat dgbulk -30.3 dhbulk -22.2 temperature 300
It produces the expected output sum.out and mydata.dat files.
I have a last question, regarding visualisation. Any clues as to which files to use with Chimera or VMD
George
> On 14 Sep 2017, at 19:34, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> This message provides the clue to what is going on:
>
> On Thu, Sep 14, 2017 at 12:04 PM, George Tzotzos <gtzotzos.me.com <mailto: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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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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>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
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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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>>
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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 <https://www.lobos.nih.gov/lcb>
>
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Received on Thu Sep 14 2017 - 10:00:04 PDT
