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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 14 2017 - 09:00:05 PDT
