[AMBER] Volmap command in cpptraj followed by SPAM

From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Date: Thu, 23 May 2019 13:59:28 +0000

Hi everyone,


I have a system containing a protein in water+acetonitrile mixture . concentration of acetonitrile (C3N) ~1M in the box.

I was trying to get the density peaks (maximum occupancy of the C3N molecules) using volmap command, using the default peakcut of 0.05 I get no peaks. SO when I changed the peakcut to 0.001 I got 38 peaks with C3N density

Now I ran the SPAM analysis using dgbulk -30.134kcal/mol and dhbulk -16.304 kcal/mol (which i calculated from the mixed boxes of solvents) and I get the following spam_summary.out:

These are the contents
#Peak SPAM_00001[DG] SPAM_00001[DH] SPAM_00001[-TDS]
   1.000 1.1239 -4.2699 5.3939
   2.000 3.9976 -2.5628 6.5604
   3.000 4.2559 -4.4379 8.6938
   4.000 2.8996 -3.7848 6.6845
   5.000 4.1529 -3.8566 8.0095
   6.000 5.2417 -2.9198 8.1616
   7.000 5.2528 -4.3155 9.5683
   8.000 4.9344 -4.0187 8.9531
   9.000 4.2121 -3.1522 7.3643
  10.000 1.2589 -5.6480 6.9069
  11.000 3.8040 -3.1885 6.9926
  12.000 2.0399 -5.1023 7.1422
  13.000 9.5173 -0.5348 10.0521
  14.000 12.6076 2.0173 10.5903
  15.000 4.0123 -4.6923 8.7046
  16.000 2.4837 -4.1886 6.6724
  17.000 2.6848 -5.9741 8.6588
  18.000 3.2674 -2.9996 6.2670
  19.000 9.6573 0.6145 9.0428
  20.000 1.0695 -6.1519 7.2214
  21.000 2.0154 -3.4040 5.4193
  22.000 4.5335 -3.4680 8.0014
  23.000 3.3508 -4.5588 7.9096
  24.000 4.8035 -4.6952 9.4987
  25.000 4.0905 -3.5317 7.6222
  26.000 6.4705 -1.8507 8.3212
  27.000 7.0362 -1.6660 8.7022
  28.000 2.2571 -5.1272 7.3844
  29.000 6.8969 -1.4719 8.3688
  30.000 0.5128 -6.0684 6.5812
  31.000 1.0279 -6.4657 7.4936
  32.000 2.6101 -5.0181 7.6282
  33.000 10.4349 -0.3935 10.8284
  34.000 3.3904 -4.1463 7.5368
  35.000 0.9351 -4.8690 5.8041
  36.000 3.0214 -5.0104 8.0317


I have few queries on these results

  1. All the peaks have net + free energies (unfavorable) , the dH values are all negative but the entropies are hugely positive, how to give a physical explanation for these values?
  2. Does the above data mean that there are no favorable interactions between the C3N probes with the protein?
  3. Any explanation to understand and interpret the data obtained will be very helpful


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Received on Thu May 23 2019 - 07:00:03 PDT
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