Dear Amber users,
I would like to calculate drift of small ligand on the surface of the receptor. I mean averaged displacement during simulation period against the initial position in the binding site.
How is better to do this? I see three relevant commands: calculation of RMS, calculation of atomic fluctuations and diffusion.
I've used the next PRAJ script to calculate these paratemres for 245 residue (small molecule ligand):
"trajin 34139_md2.mdcrd strip: WAT
rms first out 34139_ca.rms :245.CA time 10
diffusion :245.C,CA,N time 10 average filenameroot_1.xmgr
atomicfluct out 34139.apf :245.C,CA,N byatom "
RMS: will mostly show rms from atomic coordinates of ligand's atoms.
The atomic fluctuations calculation probably is a solution? But I get error with it:
"PTRAJ ATOMICFLUCT: Dumping atomic positional fluctuations
Segmentation fault"
Diffusion: diffusion can show averaged square replacements of atoms in the mask.
"Also, this command implicitly unfolds the trajectory (in periodic boundary simulations) hence
will currently only work with orthorhombic unit cells." So if I use explicit solvent I can't use this command?
For diffusion command I've got the results which I can't interpret.
The average displacement of central of mass of the ligand is about 1 angsatrom maimum, but I get some where big values in xmgr files output, which I can't understand (shown below).
Sincerely yours,
Andrew
10_a.xmgr:
0.000 5.009
0.000 7.003
0.000 8.565
0.000 9.834
0.000 10.968
0.000 11.947
0.000 12.857
0.000 13.702
0.000 14.485
0.000 15.236
0.000 15.959
0.000 16.716
0.000 17.333
0.000 17.959
0.000 18.528
0.000 19.135
0.000 19.719
0.000 20.290
0.000 20.826
0.000 21.331
0.000 21.805
0.000 22.327
0.000 22.828
0.000 23.350
0.000 23.784
0.000 24.250
0.000 24.697
0.000 25.122
0.000 25.587
0.000 25.979
0.000 26.415
0.000 26.827
0.000 27.232
0.000 27.661
0.000 28.028
0.000 28.424
0.000 28.784
0.000 29.179
0.000 29.520
0.000 29.897
0.000 30.235
0.000 30.585
0.000 30.943
0.000 31.337
0.000 31.706
0.000 32.036
0.000 32.369
0.000 32.740
0.000 33.085
0.000 33.462
0.000 33.848
0.000 34.191
0.000 34.506
0.000 34.866
0.000 35.155
0.000 35.460
0.000 35.785
0.000 36.087
0.000 36.333
0.000 36.629
0.000 36.905
0.000 37.147
0.000 37.422
0.000 37.699
0.000 38.055
0.000 38.349
0.000 38.606
0.000 38.836
0.000 39.150
0.000 39.401
0.000 39.701
0.000 39.980
0.000 40.237
0.000 40.564
0.000 40.791
0.000 41.005
0.000 41.261
0.000 41.524
0.000 41.717
0.000 42.022
0.000 42.291
0.000 42.581
0.000 42.762
0.000 43.024
0.000 43.254
0.000 43.579
0.000 43.833
0.000 44.070
0.000 44.348
0.000 44.597
0.000 44.867
0.000 45.224
0.000 45.440
0.000 45.630
0.000 45.879
0.000 46.115
0.000 46.423
0.000 46.631
0.000 46.848
10_r.xmgr:
0.000 25.088
0.000 49.043
0.000 73.355
0.000 96.703
0.000 120.287
0.000 142.741
0.000 165.302
0.000 187.739
0.000 209.802
0.000 232.141
0.000 254.688
0.000 279.422
0.000 300.450
0.000 322.530
0.000 343.271
0.000 366.148
0.000 388.838
0.000 411.687
0.000 433.723
0.000 455.013
0.000 475.463
0.000 498.476
0.000 521.116
0.000 545.241
0.000 565.684
0.000 588.041
0.000 609.953
0.000 631.106
0.000 654.700
0.000 674.914
0.000 697.750
0.000 719.678
0.000 741.608
0.000 765.110
0.000 785.568
0.000 807.951
0.000 828.518
0.000 851.437
0.000 871.409
0.000 893.801
0.000 914.146
0.000 935.466
0.000 957.464
0.000 981.996
0.000 1005.288
0.000 1026.333
0.000 1047.739
0.000 1071.890
0.000 1094.618
0.000 1119.674
0.000 1145.712
0.000 1169.050
0.000 1190.650
0.000 1215.642
0.000 1235.865
0.000 1257.410
0.000 1280.536
0.000 1302.253
0.000 1320.118
0.000 1341.713
0.000 1361.944
0.000 1379.910
0.000 1400.441
0.000 1421.219
0.000 1448.205
0.000 1470.671
0.000 1490.406
0.000 1508.244
0.000 1532.715
0.000 1552.447
0.000 1576.157
0.000 1598.408
0.000 1619.037
0.000 1645.472
0.000 1663.925
0.000 1681.436
0.000 1702.437
0.000 1724.278
0.000 1740.302
0.000 1765.807
0.000 1788.493
0.000 1813.160
0.000 1828.612
0.000 1851.107
0.000 1870.924
0.000 1899.128
0.000 1921.351
0.000 1942.189
0.000 1966.704
0.000 1988.871
0.000 2013.065
0.000 2045.233
0.000 2064.797
0.000 2082.126
0.000 2104.865
0.000 2126.576
0.000 2155.103
0.000 2174.421
0.000 2194.749
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Received on Mon Feb 15 2010 - 06:30:02 PST
