Calculation of J-couplings from molecular dynamics trajectories

Coefficients for the various forms of Karplus equation come from Graf J, Nguyen PH, Stock G, Schwalbe H. (2007), with a correction for 3J(HN,C'). DFT1 and DFT2 variations come from Best RB, Buchete NV, Hummer G. (2008). These, in turn, come from Hu & Bax (1997), and Case, Scheurer, Brüschweiler (2000). See the source code at the end of this page for the actual equations used.

On the technical front proceed as follows:

# 
# 
# d
total 2335384
-r--r--r-- 1 glykos glykos 2391410376 Jul 19 16:25 my.dcd
-r--r--r-- 1 glykos glykos      17061 Jul 19 16:25 my.psf
# 
# 
# phi_psi_indeces < my.psf
Found 21 N-CA-C atoms ...
Will change order of atoms for residue 7
     1      5     11     13  # psi for residue    1
    11     13     15     21  # phi for residue    2
    13     15     21     23  # psi for residue    2
    21     23     25     31  # phi for residue    3
    23     25     31     33  # psi for residue    3
    31     33     35     41  # phi for residue    4
    33     35     41     43  # psi for residue    4
    41     43     45     51  # phi for residue    5
    43     45     51     53  # psi for residue    5
    51     53     55     61  # phi for residue    6
    53     55     61     66  # psi for residue    6
    61     66     68     63  # phi for residue    7
# 
# cat > TORS
     1      5     11     13  # psi for residue    1
    11     13     15     21  # phi for residue    2
    13     15     21     23  # psi for residue    2
    21     23     25     31  # phi for residue    3
    23     25     31     33  # psi for residue    3
    31     33     35     41  # phi for residue    4
    33     35     41     43  # psi for residue    4
    41     43     45     51  # phi for residue    5
    43     45     51     53  # psi for residue    5
    51     53     55     61  # phi for residue    6
    53     55     61     66  # psi for residue    6
    61     66     68     63  # phi for residue    7
<CTRL-D>
# 
# 
# carma -v -atmid ALLID -tors TORS my.dcd my.psf 

carma v.1.1____________________________________________________________________

73 atoms are declared in the PSF file.
It appears that this DCD file contains unit cell information.
Number of coordinate sets is 2501475
Starting timestep         is 0
Timesteps between sets    is 1
Titles : 
Created by DCD plugin
REMARKS Created 12 February, 2011 at 16:26
Number of atoms in sets   is 73
Read 12 tetraplets for torsion calculation.
Now processing frame  2501475
End of DCD reached. All done.
#
#
# d
total 2649540
-rw-r--r-- 1 glykos glykos        624 Jul 19 16:35 TORS
-rw-r--r-- 1 glykos glykos  321690276 Jul 19 16:36 carma.torsions
-r--r--r-- 1 glykos glykos 2391410376 Jul 19 16:25 my.dcd
-r--r--r-- 1 glykos glykos      17061 Jul 19 16:25 my.psf
#
#
# head carma.torsions 
      1 +119.1116 -154.1341 +169.6075 -156.5038 +157.8043 -148.7075 +160.3349 -163.0390 +150.4241 -158.0055 +151.2057 -127.3829
      2 +124.7081 -164.5483 +173.3533 -153.6879 +158.6949 -136.3921 +179.3952 -147.6533 +155.4385 -150.3319 +136.0079 -128.1866
      3 +123.2161 -163.0068 +172.6600 -152.3675 -179.0150 -156.5759 +178.1448 -149.4263 +157.2094 -153.1906 +163.2408 -149.4959
      4 +121.3624 -131.8181 +163.1223 -151.3879 +178.8408 -153.5329 +174.0991 -153.3173 +147.1957 -147.5510 +171.6891 -151.6907
      5 +170.5063 -159.6939 +162.9019 -144.1320 +172.4928 -174.2097 +153.6709 -146.6808 +151.7860 -169.9518 +146.4125 -130.3844
      6 -178.9177 -137.4126 +175.3696 -167.0806 +170.9296 -165.3637 +156.4793 -142.1590 +135.5357 -157.0344 +169.0290 -142.6736
      7 +178.0601 -157.5724 +165.5002 -161.5268 +159.9444 -150.7171 +152.1292 -140.1879 +141.9118 -165.7136 +170.0406 -151.4045
      8 +177.1025 -104.5721 +153.9745 -153.8755 +161.7823 -162.8928 -178.2787 -170.5023 +146.8703 -168.1461 +167.5059 -137.1666
      9 -167.6573 -138.4096 +179.0231 -164.8643 +151.3583 -163.1499 +163.1734 -146.7291 +164.1811 -161.1500 -178.7138 -164.8451
     10 +165.8037 -147.2730 +134.5039 -147.0755 +151.9653 -153.4375 +149.0240  -93.9799 +152.5918 -156.1689 +155.8886 -170.5973
# 
#
#
#
# calc_Jcouplings carma.torsions 
Now processing line   2501475

Residue 2
-----------
3J(HN,HA)  6.511 ( 2.171)
3J(HN,HA)  6.325 ( 2.836) DFT1
3J(HN,HA)  6.676 ( 2.605) DFT2
3J(HN,C')  1.312 ( 0.938)
3J(HN,C')  1.404 ( 1.249) DFT1
3J(HN,C')  1.226 ( 1.284) DFT2
3J(HA,C')  2.173 ( 1.499)
3J(HA,C')  2.019 ( 1.545) DFT1
3J(HA,C')  2.213 ( 1.611) DFT2
3J(C',C')  1.001 ( 0.790)
3J(C',C')  0.969 ( 1.195) DFT1
3J(C',C')  1.046 ( 1.161) DFT2
3J(HN,CB)  1.568 ( 0.918)
3J(HN,CB)  2.838 ( 2.056) DFT1
3J(HN,CB)  2.245 ( 1.675) DFT2
1J(N,CA)  10.850 ( 0.948)
2J(N,AA)   8.585 ( 0.317)
3J(HN,CA)  0.598 ( 0.211)


Residue 3
-----------
3J(HN,HA)  6.563 ( 2.201)
3J(HN,HA)  6.387 ( 2.872) DFT1
3J(HN,HA)  6.798 ( 2.655) DFT2
3J(HN,C')  1.213 ( 0.915)
3J(HN,C')  1.270 ( 1.210) DFT1
3J(HN,C')  1.089 ( 1.228) DFT2
3J(HA,C')  2.147 ( 1.439)
3J(HA,C')  2.001 ( 1.496) DFT1
3J(HA,C')  2.202 ( 1.564) DFT2
3J(C',C')  0.946 ( 0.741)
3J(C',C')  0.880 ( 1.119) DFT1
3J(C',C')  0.953 ( 1.089) DFT2
3J(HN,CB)  1.614 ( 0.892)
3J(HN,CB)  2.961 ( 1.981) DFT1
3J(HN,CB)  2.336 ( 1.621) DFT2
1J(N,CA)  10.687 ( 0.910)
2J(N,AA)   7.628 ( 1.228)
3J(HN,CA)  0.528 ( 0.222)


Residue 4
-----------
3J(HN,HA)  6.771 ( 2.114)
3J(HN,HA)  6.675 ( 2.759) DFT1
3J(HN,HA)  6.996 ( 2.566) DFT2
3J(HN,C')  1.206 ( 0.941)
3J(HN,C')  1.271 ( 1.254) DFT1
3J(HN,C')  1.145 ( 1.290) DFT2
3J(HA,C')  2.344 ( 1.622)
3J(HA,C')  2.212 ( 1.641) DFT1
3J(HA,C')  2.422 ( 1.705) DFT2
3J(C',C')  0.994 ( 0.772)
3J(C',C')  0.949 ( 1.171) DFT1
3J(C',C')  1.019 ( 1.140) DFT2
3J(HN,CB)  1.533 ( 0.897)
3J(HN,CB)  2.738 ( 1.998) DFT1
3J(HN,CB)  2.158 ( 1.626) DFT2
1J(N,CA)  10.650 ( 0.906)
2J(N,AA)   7.370 ( 1.275)
3J(HN,CA)  0.504 ( 0.221)


Residue 5
-----------
3J(HN,HA)  6.947 ( 2.145)
3J(HN,HA)  6.883 ( 2.793) DFT1
3J(HN,HA)  7.283 ( 2.627) DFT2
3J(HN,C')  1.092 ( 0.943)
3J(HN,C')  1.128 ( 1.251) DFT1
3J(HN,C')  0.990 ( 1.261) DFT2
3J(HA,C')  2.229 ( 1.378)
3J(HA,C')  2.125 ( 1.428) DFT1
3J(HA,C')  2.345 ( 1.494) DFT2
3J(C',C')  0.981 ( 0.741)
3J(C',C')  0.920 ( 1.125) DFT1
3J(C',C')  0.979 ( 1.099) DFT2
3J(HN,CB)  1.530 ( 0.875)
3J(HN,CB)  2.797 ( 1.934) DFT1
3J(HN,CB)  2.187 ( 1.580) DFT2
1J(N,CA)  10.618 ( 0.867)
2J(N,AA)   7.252 ( 1.291)
3J(HN,CA)  0.499 ( 0.217)


Residue 6
-----------
3J(HN,HA)  7.282 ( 2.118)
3J(HN,HA)  7.335 ( 2.750) DFT1
3J(HN,HA)  7.563 ( 2.636) DFT2
3J(HN,C')  1.191 ( 1.008)
3J(HN,C')  1.282 ( 1.345) DFT1
3J(HN,C')  1.217 ( 1.353) DFT2
3J(HA,C')  2.444 ( 1.520)
3J(HA,C')  2.370 ( 1.534) DFT1
3J(HA,C')  2.595 ( 1.598) DFT2
3J(C',C')  1.139 ( 0.802)
3J(C',C')  1.157 ( 1.222) DFT1
3J(C',C')  1.215 ( 1.191) DFT2
3J(HN,CB)  1.319 ( 0.892)
3J(HN,CB)  2.300 ( 1.964) DFT1
3J(HN,CB)  1.786 ( 1.597) DFT2
1J(N,CA)  10.900 ( 0.885)
2J(N,AA)   7.131 ( 1.314)
3J(HN,CA)  0.513 ( 0.217)


Residue 7
-----------
3J(HN,HA)  8.142 ( 1.621)
3J(HN,HA)  8.396 ( 2.112) DFT1
3J(HN,HA)  8.942 ( 1.953) DFT2
3J(HN,C')  0.566 ( 0.764)
3J(HN,C')  0.480 ( 1.043) DFT1
3J(HN,C')  0.421 ( 1.036) DFT2
3J(HA,C')  2.221 ( 0.477)
3J(HA,C')  2.268 ( 0.650) DFT1
3J(HA,C')  2.549 ( 0.712) DFT2
3J(C',C')  0.994 ( 0.628)
3J(C',C')  0.886 ( 0.968) DFT1
3J(C',C')  0.899 ( 0.963) DFT2
3J(HN,CB)  1.365 ( 0.758)
3J(HN,CB)  2.610 ( 1.627) DFT1
3J(HN,CB)  1.962 ( 1.335) DFT2
1J(N,CA)   0.000 ( 0.000)
2J(N,AA)   7.536 ( 1.330)
3J(HN,CA)  0.590 ( 0.187)


#
#
#

and copy-paste the results to a file.



The programs (other than the latest β version of carma) that you need to make this happen live in /usr/local/bin. Their source code is :

phi_psi_indeces , a perl script to generate a list of atom indeces for φ, ψ angles suitable for carma

calc_Jcouplings , a perl script to read a list of φ, ψ angles and calculate J-couplings

research/howto/md_and_nmr_calculation_of_j-couplings.txt · Last modified: 2012/01/05 17:29 by glykos