Below is the output.
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 name TEST cut 12 summary sum.out dgbulk -30.3 dhbulk -22.2 temperature 300]
Warning: 'dgbulk' not specified; using default for SPC/E water.
Warning: 'dhbulk' not specified; using default for SPC/E water.
SPAM:
Solvent [WAT] density peaks taken from mypeakfile.xyz.
727 density peaks will be analyzed from mypeakfile.xyz.
Occupation information printed to spam.info.
Sites are boxes with edge length 1.250
Re-ordering trajectory so each site always has the same water molecule.
Not calculating any SPAM energies
#Citation: Cui, G.; Swails, J.M.; Manas, E.S.; "SPAM: A Simple Approach
# for Profiling Bound Water Molecules"
# J. Chem. Theory Comput., 2013, 9 (12), pp 5539–5549.
[run]
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: subA_solv.prmtop, 13140 atoms, 3847 res, box: Trunc. Oct., 3723 mol, 3713 solvent
INPUT TRAJECTORIES (1 total):
0: 'prod_100ns.nc' is a NetCDF AMBER trajectory, Parm subA_solv.prmtop (Trunc. Oct. box) (reading 10000 of 10000)
Coordinate processing will occur on 10000 frames.
BEGIN TRAJECTORY PROCESSING:
.....................................................
ACTION SETUP FOR PARM 'subA_solv.prmtop' (1 actions):
0: [spam mypeakfile.xyz solv WAT reorder name TEST cut 12 summary sum.out dgbulk -30.3 dhbulk -22.2 temperature 300]
Found 3713 solvent residues [WAT]
----- prod_100ns.nc (1-10000, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 10000 frames and processed 10000 frames.
TIME: Avg. throughput= 39.8055 frames / second.
ACTION OUTPUT:
SPAM timing data:
TIME: Residue c.o.m. calc: 0.4506 s ( 0.18%)
TIME: Peak assignment : 248.4293 s ( 99.72%)
TIME: Occupancy calc. : 0.1642 s ( 0.07%)
TIME: Energy calc : 0.0004 s ( 0.00%)
TIME: Residue reordering : 0.0797 s ( 0.03%)
TIME: SPAM Action Total: 249.1271 s
Warning: No energies for 727 peaks.
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
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> 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 - 09:30:03 PDT
