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
