AMBER Archive (2003)

Subject: Residual dipolar couplings

From: McAteer, Kathleen (Kathleen.McAteer_at_pnl.gov)
Date: Wed Apr 30 2003 - 12:56:34 CDT

Has anyone else experienced problems reading residual dipolar coupling restraints in AMBER 7? My input file for RDCs is shown below:

&align ndip=12, dcut=-1.0, gigj=-3.163, s11=-10.0, s22=-10.0, s12=0.0, s13=0.0, s23=0.0, id(1)=48, jd(1)=49, dobs(1)= 9.82, id(2)=111, jd(2)=112, dobs(2)= 9.74, id(3)=302, jd(3)=303, dobs(3)= 9.80, id(4)=365, jd(4)=366, dobs(4)= 9.82, id(5)=427, jd(5)=428, dobs(5)= 9.82, id(6)=490, jd(6)=491, dobs(6)= 9.74, id(7)=681, jd(7)=682, dobs(7)= 9.80, id(8)=744, jd(8)=745, dobs(8)= 9.82, id(9)=211, jd(9)=212, dobs(9)= 9.93, id(10)=243, jd(10)=244, dobs(10)= 9.96, id(11)=590, jd(11)=591, dobs(11)= 9.55, id(12)=622, jd(12)=623, dobs(12)= 9.59, &end
The output file from SANDER indicates that the RDCs are being read but the program is not using them properly:

Residual dipolar splittings:

 ------------------------------------------------------------------------------
 First atom Last atom curr. value target deviation penalty distance
 ------------------------------------------------------------------------------
 N1 DG 2 -- H1 DG 2: -2.235 9.820 -12.055 145.315 1.016
 N1 DG 4 -- H1 DG 4: 0.000 9.740 -9.740 94.868 1.016
 N1 DG 10 -- H1 DG 10: 0.000 9.800 -9.800 96.040 1.016
 N1 DG3 12 -- H1 DG3 12: 0.000 9.820 -9.820 96.432 1.016
 N1 DG 14 -- H1 DG 14: 0.000 9.820 -9.820 96.432 1.016
 N1 DG 16 -- H1 DG 16: 0.000 9.740 -9.740 94.868 1.016
 N1 DG 22 -- H1 DG 22: 0.000 9.800 -9.800 96.040 1.015
 N1 DG3 24 -- H1 DG3 24: 0.000 9.820 -9.820 96.432 1.016
 N3 DT 7 -- H3 DT 7: 0.000 9.930 -9.930 98.605 1.016
 N3 DT 8 -- H3 DT 8: 0.000 9.960 -9.960 99.202 1.015
 N3 DT 19 -- H3 DT 19: 0.000 9.550 -9.550 91.203 1.016
 N3 DT 20 -- H3 DT 20: 0.000 9.590 -9.590 91.968 1.015
                                        Total align constraint: 1197.40
                                                                                
                     # Pearson r rms error
                  -----------------------------------
Align correlation: 12 -0.09974 -0.10007 9.98918
 Diagonalize the alignment matrix:
      -10.00000 1.00000 0.00000 0.00000
      -10.00000 0.00000 1.00000 0.00000
       20.00000 0.00000 0.00000 1.00000
 Diagonalize the moment of interia tensor:
   314576.87156 0.01312 -0.04037 0.99910 25.83657
  1113221.88898 -0.30873 0.95020 0.04245 10.87709
  1142729.38719 -0.95106 -0.30901 0.00000 9.90046
 ------------------------------------------------------------------------------

If I use these same restraints with AMBER 6 I get a reasonable result so I was wondering if anyone else has had this problem.
Thanks,

Kate

Kathleen McAteer
Pacific Northwest National Laboratory
Richland, WA 99352

(509)373-5148

kathleen.mcateer_at_pnl.gov