[gmx-users] B-factor

Tue Jun 29 07:49:46 CEST 2010

Dear Erik Marklund
thanks for your attention

I saw www.pdb.org. there is b-factor in pdb files being in this website but
pdb file obtained form g_rmsf  -f  pr.xtc  -s  pr.tpr  -n  pr.ndx -oq
command, has not B-factor.

my bfac.pdb file is as follows :

TITLE Protein in water

REMARK THIS IS A SIMULATION BOX

CRYST1 62.008 62.008 62.008 90.00 90.00 90.00 P 1 1

MODEL 1

ATOM 5 CA NGL 1 20.794 51.547 38.010 1.00272.65

ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41

ATOM 23 CA SER 3 25.254 48.487 33.290 1.00189.09

ATOM 34 CA GLY 4 28.474 47.777 31.510 1.00114.27

ATOM 41 CA SER 5 27.814 48.657 27.860 1.00195.51

ATOM 52 CA SER 6 31.164 48.167 26.020 1.00217.99

ATOM 63 CA GLY 7 31.934 49.987 22.770 1.00300.70

ATOM 70 CA LYP 8 32.204 48.057 19.510 1.00248.64

ATOM 92 CA GLY 9 35.314 45.957 18.630 1.00184.40

ATOM 99 CA GLY 10 37.064 42.607 19.150 1.00139.99

ATOM 106 CA GLN 11 37.224 39.007 17.810 1.00106.39

ATOM 123 CA VAL 12 34.754 36.657 19.540 1.00 78.29

ATOM 139 CA ARG 13 33.244 33.847 17.550 1.00 79.41

ATOM 163 CA PHE 14 32.044 30.277 17.980 1.00 23.96

ATOM 183 CA SER 15 30.254 27.737 15.740 1.00 44.68

ATOM 194 CA ASN 16 26.794 26.277 16.430 1.00 54.17

ATOM 208 CA ASP 17 28.154 23.097 18.090 1.00 52.38

ATOM 220 CA GLN 18 30.914 24.937 19.880 1.00 25.27

ATOM 237 CA THR 19 28.404 27.377 21.340 1.00 24.72

ATOM 251 CA ILE 20 26.264 24.487 22.620 1.00 35.92

ATOM 270 CA GLU 21 29.004 22.497 24.430 1.00 22.96

ATOM 285 CA LEU 22 30.324 25.797 25.950 1.00 13.17

ATOM 304 CA GLU 23 26.874 26.467 27.560 1.00 26.01

ATOM 319 CA LYP 24 26.474 22.877 28.710 1.00 37.38

ATOM 341 CA LYP 25 29.944 22.657 30.270 1.00 29.72

ATOM 363 CA PHE 26 29.484 26.037 32.040 1.00 33.01

ATOM 383 CA GLU 27 26.304 24.837 33.730 1.00 56.55

ATOM 398 CA THR 28 28.194 21.907 35.400 1.00 71.22

ATOM 412 CA GLN 29 31.264 24.057 36.290 1.00 61.11

ATOM 429 CA LYP 30 31.314 27.927 35.980 1.00 53.89

ATOM 451 CA TYR 31 35.124 27.747 35.600 1.00 54.07

ATOM 472 CA LEU 32 37.594 25.107 34.310 1.00 52.72

ATOM 491 CA SER 33 40.974 24.187 35.600 1.00 49.43

ATOM 510 CA PRO 34 43.864 24.147 33.110 1.00 41.67

ATOM 524 CA PRO 35 44.074 20.337 32.590 1.00 46.11

ATOM 530 CA GLU 36 40.404 20.317 31.650 1.00 30.32

ATOM 545 CA ARG 37 40.464 23.597 29.640 1.00 17.05

ATOM 569 CA LYP 38 43.434 22.497 27.460 1.00 19.61

ATOM 591 CA ARG 39 41.524 19.337 26.310 1.00 21.22

ATOM 615 CA LEU 40 38.184 21.167 25.940 1.00 10.93

ATOM 634 CA ALA 41 39.834 23.657 23.510 1.00 10.81

ATOM 644 CA LYP 42 41.344 20.617 21.670 1.00 20.84

ATOM 666 CA MET 43 38.004 18.787 21.490 1.00 19.62

ATOM 683 CA LEU 44 35.884 21.877 20.620 1.00 16.95

ATOM 702 CA GLN 45 38.504 23.247 18.140 1.00 23.14

ATOM 719 CA LEU 46 38.814 26.507 20.170 1.00 17.31

ATOM 738 CA SER 47 41.784 28.247 21.770 1.00 22.52

ATOM 749 CA GLU 48 42.464 28.237 25.540 1.00 18.67

ATOM 764 CA ARG 49 41.984 32.017 25.510 1.00 22.59

ATOM 788 CA GLN 50 38.484 31.627 24.050 1.00 17.42

ATOM 805 CA VAL 51 37.614 28.917 26.620 1.00 8.87

ATOM 821 CA LYP 52 38.664 31.067 29.630 1.00 15.01

ATOM 843 CA THR 53 37.104 34.267 28.220 1.00 21.29

ATOM 857 CA TRP 54 33.794 32.697 27.320 1.00 15.97

ATOM 881 CA PHE 55 33.164 31.167 30.720 1.00 16.56

ATOM 901 CA GLN 56 34.244 34.267 32.580 1.00 27.30

ATOM 918 CA ASN 57 31.854 36.577 30.640 1.00 31.82

ATOM 932 CA ARG 58 29.204 33.887 30.940 1.00 28.78

ATOM 956 CA ARG 59 29.414 34.027 34.740 1.00 42.57

ATOM 980 CA ALA 60 28.834 37.777 34.520 1.00 52.64

ATOM 990 CA LYP 61 25.674 36.957 32.590 1.00 47.32

ATOM 1012 CA TRP 62 24.714 34.207 35.090 1.00109.93

ATOM 1036 CA ARG 63 25.094 36.337 38.210 1.00145.64

ATOM 1060 CA ARG 64 22.154 38.367 36.850 1.00409.17

ATOM 1084 CA SER 65 19.994 35.337 36.560 1.00567.55

ATOM 1095 CA GLY 66 20.044 34.427 40.200 1.00313.57

ATOM 1110 CA PRO 67 22.124 34.867 43.420 1.00232.72

ATOM 1116 CA SER 68 22.484 31.017 43.640 1.00296.77

ATOM 1127 CA SER 69 26.064 29.747 43.910 1.00746.26

ATOM 1138 CA CGL 70 26.794 26.717 41.750 1.001312.96

TER

ENDMDL
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