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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--
-------------------------
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 - 08:30:06 PDT
