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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Received on Thu Sep 14 2017 - 09:00:02 PDT
