From: gurunath katagi (gurukatagi_at_gmail.com)
Date: Wed Dec 09 2009 - 04:41:11 CST

Hi ..
The RMSD values calculated are exactly equal for all chains .
I checked whether I am getting the right atoms after atom selection, it is
indeed i am getting different atom indices for the different chain
selections.

The procedure that i have followed is as follows :
mol load psf protein.psf
mol addfile protein_wb.dcd

# for chain A

source residue_rmsd-a.tcl

#make a selection of the atoms in the individual chains

set sel_resid1 [[atomselect top "protein and chain A and alpha"] get resid]

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28
29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53
54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78
79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102
103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121
122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140
141

rmsd_residue_over_time top $sel_resid1

# for the sake of checking the atom selection, i have written the pdb file
and
# the indices of the selection as
set sel_resid2 [atomselect top "protein and chain A and alpha"]
$sel_resid2 writepdb chainA.pdb

# chain A file can be found in the attachment.
# to check the indices
set sel_resid3 [[atomselect top "protein and chain A and alpha"] get index]
4 20 39 52 64 74 86 108 122 136 152 174 184 194 218 225 247 263 270 280 297
307 314 329 350 357 367 382 392 411 426 450 467 487 506 517 539 551 565 579
601 615 636 658 670 687 707 719 738 749 766 773 784 794 811 827 849 856 873
880 902 924 940 950 962 972 991 1005 1019 1029 1045 1055 1072 1088 1100 1112
1131 1143 1157 1167 1186 1197 1207 1226 1237 1249 1268 1285 1295 1312 1334
1353 1377 1393 1407 1419 1435 1449 1469 1491 1510 1529 1540 1557 1568 1587
1606 1622 1636 1655 1665 1675 1692 1713 1725 1735 1750 1770 1786 1798 1808
1824 1841 1851 1862 1881 1893 1915 1935 1954 1964 1975 1991 2002 2016 2032
2051 2065 2076 2098 2122

# similarly for chain B
set sel_resid3 [[atomselect top "protein and chain B and alpha"] get index]
2146 2162 2179 2198 2214 2226 2241 2256 2278 2289 2299 2315 2329 2339 2358
2382 2389 2411 2427 2441 2457 2469 2484 2500 2507 2514 2529 2539 2558 2565
2589 2608 2627 2643 2659 2682 2694 2718 2732 2749 2773 2793 2813 2828 2839
2859 2866 2878 2897 2908 2924 2936 2948 2958 2974 2991 2998 3014 3026 3048
3064 3086 3096 3113 3120 3142 3164 3180 3199 3206 3216 3236 3247 3259 3266
3285 3295 3312 3331 3343 3357 3376 3398 3405 3419 3439 3449 3463 3482 3493
3508 3527 3544 3555 3567 3589 3608 3625 3641 3655 3667 3682 3696 3716 3740
3759 3778 3785 3799 3815 3834 3850 3861 3877 3896 3906 3923 3940 3960 3967
3989 4004 4024 4040 4054 4066 4082 4099 4109 4119 4140 4157 4179 4195 4211
4221 4228 4244 4254 4268 4278 4297 4307 4324 4346 4370

Please download the files from the following link:
https://ssl.serc.iisc.ernet.in/~gurunath/rmsd.tar.gz

I have sent the config file, dcd file and directory named res_rmsd which
containing the rmsd files for each chain.
eg : residue_rmsd-chain-a.dat -- rmsd values for chain A

Please check notes.txt for futher details.

Thank you
Gurunath