Hi,
Try adding something like 'centermask !:1-153' to the volmap command,
and use :WAT.O instead of :WAT (should be a bit more efficient). Also
note that since the peaks file is not generate until the trajectory
processing run is completed, you really should be doing this in 2
passes; 1 to generate the peaks file, and the second to perform spam
analysis. E.g.
parm ./setup/ACN_IL1B_solvated.prmtop
trajin ./run_1/prod/ACN_IL1B_production4F.mdcrd 1 1250
# First pass to generate peaks
rms first :1-153
center :1-153 mass origin
volmap volmap.xplor 0.5 0.5 0.5 :WAT.O radscale 1.0 name GRID size
10,10,10 peakcut 0.001 peakfile peaks.xyz centermask !:1-153
run
# Second pass to run SPAM
rms first :1-153
center :1-153 mass origin
spam peaks.xyz solv WAT reorder cut 12 sphere site_size 2.5 info
info.txt summary spam_summary.out out spam_energies.out dgbulk -28.459
dhbulk -17.741
run
Hope this helps,
-Dan
On Tue, Mar 5, 2019 at 5:05 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> Hi,
> Whatever spam input file I use I am always getting no density peaks found in n frames ( whether my frames is 10 or 10000).
> My input file is
> parm ./setup/ACN_IL1B_solvated.prmtop
> trajin ./run_1/prod/ACN_IL1B_production4F.mdcrd 1 1250
> rms first :1-153
> center :1-153 mass origin
> volmap volmap.xplor 0.5 0.5 0.5 :WAT radscale 1.0 name GRID size 10,10,10 peakcut 0.001 peakfile peaks.xyz
> spam peaks.xyz solv WAT reorder cut 12 sphere site_size 2.5 info info.txt summary spam_summary.out out spam_energies.out dgbulk -28.459 dhbulk -17.741
>
>
> It cannot be that there are no densities, I get output in my peaks.xyz
>
> 10904
>
> C -43.00000000 -28.00000000 19.50000000 0.01033021
> C -42.50000000 -25.00000000 7.50000000 0.01010631
> C -42.50000000 -19.50000000 20.00000000 0.01100946
> C -42.00000000 -26.00000000 15.50000000 0.01140510
> C -41.50000000 -25.50000000 12.00000000 0.01124454
> C -41.50000000 -17.00000000 16.50000000 0.01068211
> C -40.50000000 -22.50000000 20.50000000 0.01210647
> C -40.00000000 -20.00000000 13.00000000 0.01161815
> C -39.50000000 -16.00000000 18.50000000 0.01248063
> C -36.00000000 -4.50000000 -24.50000000 0.02160235
> C -35.50000000 -22.50000000 -20.50000000 0.03389744
> C -35.50000000 -20.00000000 -25.00000000 0.03288217
> C -35.00000000 -31.50000000 -15.00000000 0.03014405
> C -35.00000000 -23.00000000 -27.50000000 0.03395218
> C -35.00000000 -21.50000000 -12.00000000 0.03401110
> C -35.00000000 -16.00000000 -14.00000000 0.03385241
> C -35.00000000 -13.50000000 -13.50000000 0.03304833
> C -35.00000000 3.00000000 -23.00000000 0.02128701
> C -35.00000000 21.00000000 -20.50000000 0.01756181
> C -34.50000000 -37.00000000 -15.00000000 0.01695646
> C -34.50000000 -28.00000000 -25.50000000 0.03471959
> C -34.50000000 -28.00000000 -22.50000000 0.03460344
> C -34.50000000 -28.00000000 -21.00000000 0.03433393
> C -34.50000000 -28.00000000 -13.00000000 0.03452293
> C -34.50000000 -25.00000000 -12.00000000 0.03372023
> C -34.50000000 -22.50000000 -23.00000000 0.03543151
> C -34.50000000 -21.50000000 -17.00000000 0.03432877
> C -34.50000000 -21.00000000 -7.00000000 0.03258215
> C -34.50000000 -19.50000000 -21.50000000 0.03361508
> C -34.50000000 -17.50000000 -16.50000000 0.03568002
> C -34.50000000 -15.00000000 -18.50000000 0.03410076
> C -34.50000000 -14.50000000 -15.00000000 0.03378885
> C -34.50000000 -13.50000000 -17.00000000 0.03376717
> C -34.50000000 -12.00000000 -11.50000000 0.03414648
> C -34.50000000 -10.00000000 -15.00000000 0.03283173
> C -34.50000000 16.00000000 -12.50000000 0.01845697
> C -34.50000000 32.00000000 -20.00000000 0.01816759
> C -34.00000000 -27.50000000 -17.50000000 0.03401608
> C -34.00000000 -26.00000000 -19.00000000 0.03456162
> C -34.00000000 -24.50000000 -17.50000000 0.03412251
> C -34.00000000 -17.00000000 -19.50000000 0.03492058
> C -34.00000000 -15.00000000 -26.00000000 0.03375600
> C -34.00000000 -14.50000000 -11.50000000 0.03431633
> C -34.00000000 -14.00000000 -7.50000000 0.03306666
> C -34.00000000 -13.50000000 -21.00000000 0.03447072
> C -34.00000000 -12.50000000 -19.00000000 0.03440037
> C -34.00000000 -10.50000000 -18.50000000 0.03374498
> C -34.00000000 -10.50000000 -8.00000000 0.03434557
> C -34.00000000 -9.00000000 -2.00000000 0.03327096
> C -34.00000000 -8.00000000 -5.50000000 0.03306337
> C -34.00000000 -6.00000000 -8.00000000 0.03447726
> C -34.00000000 4.50000000 -25.50000000 0.02152826
> C -33.50000000 -29.50000000 -27.50000000 0.03398738
> C -33.50000000 -29.00000000 -9.50000000 0.03398079
> C -33.50000000 -28.50000000 -1.50000000 0.03431878
> C -33.50000000 -28.00000000 21.50000000 0.02632517
> C -33.50000000 -26.00000000 -23.00000000 0.03461641
> C -33.50000000 -25.50000000 -9.00000000 0.03512300
> C -33.50000000 -25.00000000 -15.00000000 0.03461039
> C -33.50000000 -22.50000000 -30.50000000 0.03156000
> C -33.50000000 -20.00000000 -26.00000000 0.03375579
> C -33.50000000 -20.00000000 -20.50000000 0.03396581
> C -33.50000000 -20.00000000 -9.00000000 0.03587337
>
>
> What can be a possible issue?
> Any ideas will be very helpful.
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Received on Mon Mar 11 2019 - 12:30:04 PDT
