AMBER Archive (2007)

Subject: Re: AMBER: chem shift format

From: David A. Case (case_at_scripps.edu)
Date: Fri Nov 16 2007 - 18:00:27 CST

On Fri, Nov 16, 2007, McElheny, Dan wrote:
>
> does anyone have an example of a chemical shift restraint (&shf) for amber?

Below is one that I use, and which will be in the Amber 10 test suite.

...regards...dac

 &shf
  nring = 30,
  namr(1) = 'GUA 1 5', natr(1)=5, str(1)= 1.000,
  iatr(1,1) = 11,25,15,14,12,
  namr(2) = 'GUA 1 6', natr(2)=6, str(2)= 0.510,
  iatr(1,2) = 25,24,20,18,16,15,
  namr(3) = 'CYT 2 ', natr(3)=6, str(3)= 0.370,
  iatr(1,3) = 44,54,53,49,47,45,
  namr(4) = 'GUA 3 5', natr(4)=5, str(4)= 1.000,
  iatr(1,4) = 74,88,78,77,75,
  namr(5) = 'GUA 3 6', natr(5)=6, str(5)= 0.510,
  iatr(1,5) = 88,87,83,81,79,78,
  namr(6) = 'THY 4 ', natr(6)=6, str(6)= 0.350,
  iatr(1,6) = 107,119,117,115,110,108,
  namr(7) = 'THY 5 ', natr(7)=6, str(7)= 0.350,
  iatr(1,7) = 139,151,149,147,142,140,
  namr(8) = 'ADE 6 5', natr(8)=5, str(8)= 1.140,
  iatr(1,8) = 171,184,175,174,172,
  namr(9) = 'ADE 6 6', natr(9)=6, str(9)= 0.900,
  iatr(1,9) = 184,183,181,180,176,175,
  namr(10) = 'ADE 7 5', natr(10)=5, str(10)= 1.140,
  iatr(1,10) = 203,216,207,206,204,
  namr(11) = 'ADE 7 6', natr(11)=6, str(11)= 0.900,
  iatr(1,11) = 216,215,213,212,208,207,
  namr(12) = 'CYT 8 ', natr(12)=6, str(12)= 0.370,
  iatr(1,12) = 235,245,244,240,238,236,
  namr(13) = 'GUA 9 5', natr(13)=5, str(13)= 1.000,
  iatr(1,13) = 265,279,269,268,266,
  namr(14) = 'GUA 9 6', natr(14)=6, str(14)= 0.510,
  iatr(1,14) = 279,278,274,272,270,269,
  namr(15) = 'CYT 10 ', natr(15)=6, str(15)= 0.370,
  iatr(1,15) = 298,308,307,303,301,299,
  namr(16) = 'GUA 11 5', natr(16)=5, str(16)= 1.000,
  iatr(1,16) = 327,341,331,330,328,
  namr(17) = 'GUA 11 6', natr(17)=6, str(17)= 0.510,
  iatr(1,17) = 341,340,336,334,332,331,
  namr(18) = 'CYT 12 ', natr(18)=6, str(18)= 0.370,
  iatr(1,18) = 360,370,369,365,363,361,
  namr(19) = 'GUA 13 5', natr(19)=5, str(19)= 1.000,
  iatr(1,19) = 390,404,394,393,391,
  namr(20) = 'GUA 13 6', natr(20)=6, str(20)= 0.510,
  iatr(1,20) = 404,403,399,397,395,394,
  namr(21) = 'THY 14 ', natr(21)=6, str(21)= 0.350,
  iatr(1,21) = 423,435,433,431,426,424,
  namr(22) = 'THY 15 ', natr(22)=6, str(22)= 0.350,
  iatr(1,22) = 455,467,465,463,458,456,
  namr(23) = 'ADE 16 5', natr(23)=5, str(23)= 1.140,
  iatr(1,23) = 487,500,491,490,488,
  namr(24) = 'ADE 16 6', natr(24)=6, str(24)= 0.900,
  iatr(1,24) = 500,499,497,496,492,491,
  namr(25) = 'ADE 17 5', natr(25)=5, str(25)= 1.140,
  iatr(1,25) = 519,532,523,522,520,
  namr(26) = 'ADE 17 6', natr(26)=6, str(26)= 0.900,
  iatr(1,26) = 532,531,529,528,524,523,
  namr(27) = 'CYT 18 ', natr(27)=6, str(27)= 0.370,
  iatr(1,27) = 551,561,560,556,554,552,
  namr(28) = 'GUA 19 5', natr(28)=5, str(28)= 1.000,
  iatr(1,28) = 581,595,585,584,582,
  namr(29) = 'GUA 19 6', natr(29)=6, str(29)= 0.510,
  iatr(1,29) = 595,594,590,588,586,585,
  namr(30) = 'CYT 20 ', natr(30)=6, str(30)= 0.370,
  iatr(1,30) = 614,624,623,619,617,615,
  iprot( 1)= 170, wt( 1)= 1.0, obs( 1)= 0.650,
  iprot( 2)= 186, wt( 2)= 1.0, obs( 2)= 0.684,
  iprot( 3)= 167, wt( 3)= 1.0, obs( 3)= 0.409,
  iprot( 4)= 202, wt( 4)= 1.0, obs( 4)= 0.822,
  iprot( 5)= 218, wt( 5)= 1.0, obs( 5)= 0.638,
  iprot( 6)= 199, wt( 6)= 1.0, obs( 6)= 0.438,
  iprot( 7)= 43, wt( 7)= 1.0, obs( 7)= 0.530,
  iprot( 8)= 57, wt( 8)= 1.0, obs( 8)= 0.529,
  iprot( 9)= 40, wt( 9)= 1.0, obs( 9)= 0.226,
  iprot( 10)= 234, wt( 10)= 1.0, obs( 10)= 0.324,
  iprot( 11)= 248, wt( 11)= 1.0, obs( 11)= 0.397,
  iprot( 12)= 231, wt( 12)= 1.0, obs( 12)= 0.111,
  iprot( 13)= 182, wt( 13)= 1.0, obs( 13)= -1.765,
  iprot( 14)= 214, wt( 14)= 1.0, obs( 14)= -1.087,
  iprot( 15)= 10, wt( 15)= 1.0, obs( 15)= 0.759,
  iprot( 16)= 27, wt( 16)= 1.0, obs( 16)= 0.495,
  iprot( 17)= 7, wt( 17)= 1.0, obs( 17)= 0.258,
  iprot( 18)= 73, wt( 18)= 1.0, obs( 18)= 0.816,
  iprot( 19)= 90, wt( 19)= 1.0, obs( 19)= 0.644,
  iprot( 20)= 70, wt( 20)= 1.0, obs( 20)= 0.416,
  iprot( 21)= 264, wt( 21)= 1.0, obs( 21)= 0.702,
  iprot( 22)= 281, wt( 22)= 1.0, obs( 22)= 0.592,
  iprot( 23)= 261, wt( 23)= 1.0, obs( 23)= 0.338,
  iprot( 24)= 486, wt( 24)= 1.0, obs( 24)= 0.650,
  iprot( 25)= 502, wt( 25)= 1.0, obs( 25)= 0.684,
  iprot( 26)= 483, wt( 26)= 1.0, obs( 26)= 0.409,
  iprot( 27)= 518, wt( 27)= 1.0, obs( 27)= 0.822,
  iprot( 28)= 534, wt( 28)= 1.0, obs( 28)= 0.638,
  iprot( 29)= 515, wt( 29)= 1.0, obs( 29)= 0.438,
  iprot( 30)= 297, wt( 30)= 1.0, obs( 30)= 0.948,
  iprot( 31)= 311, wt( 31)= 1.0, obs( 31)= 0.134,
  iprot( 32)= 294, wt( 32)= 1.0, obs( 32)= 0.045,
  iprot( 33)= 48, wt( 33)= 1.0, obs( 33)= -0.805,
  iprot( 34)= 239, wt( 34)= 1.0, obs( 34)= -1.022,
  iprot( 35)= 359, wt( 35)= 1.0, obs( 35)= 0.530,
  iprot( 36)= 373, wt( 36)= 1.0, obs( 36)= 0.529,
  iprot( 37)= 356, wt( 37)= 1.0, obs( 37)= 0.226,
  iprot( 38)= 550, wt( 38)= 1.0, obs( 38)= 0.324,
  iprot( 39)= 564, wt( 39)= 1.0, obs( 39)= 0.397,
  iprot( 40)= 547, wt( 40)= 1.0, obs( 40)= 0.111,
  iprot( 41)= 613, wt( 41)= 1.0, obs( 41)= 0.948,
  iprot( 42)= 627, wt( 42)= 1.0, obs( 42)= 0.134,
  iprot( 43)= 610, wt( 43)= 1.0, obs( 43)= 0.045,
  iprot( 44)= 173, wt( 44)= 1.0, obs( 44)= -0.336,
  iprot( 45)= 205, wt( 45)= 1.0, obs( 45)= -0.497,
  iprot( 46)= 46, wt( 46)= 1.0, obs( 46)= -0.384,
  iprot( 47)= 237, wt( 47)= 1.0, obs( 47)= -0.644,
  iprot( 48)= 498, wt( 48)= 1.0, obs( 48)= -1.765,
  iprot( 49)= 530, wt( 49)= 1.0, obs( 49)= -1.087,
  iprot( 50)= 326, wt( 50)= 1.0, obs( 50)= 0.759,
  iprot( 51)= 343, wt( 51)= 1.0, obs( 51)= 0.495,
  iprot( 52)= 323, wt( 52)= 1.0, obs( 52)= 0.258,
  iprot( 53)= 389, wt( 53)= 1.0, obs( 53)= 0.816,
  iprot( 54)= 406, wt( 54)= 1.0, obs( 54)= 0.644,
  iprot( 55)= 386, wt( 55)= 1.0, obs( 55)= 0.416,
  iprot( 56)= 580, wt( 56)= 1.0, obs( 56)= 0.702,
  iprot( 57)= 597, wt( 57)= 1.0, obs( 57)= 0.592,
  iprot( 58)= 577, wt( 58)= 1.0, obs( 58)= 0.338,
  iprot( 59)= 302, wt( 59)= 1.0, obs( 59)= -0.769,
  iprot( 60)= 364, wt( 60)= 1.0, obs( 60)= -0.805,
  iprot( 61)= 555, wt( 61)= 1.0, obs( 61)= -1.022,
  iprot( 62)= 618, wt( 62)= 1.0, obs( 62)= -0.769,
  iprot( 63)= 13, wt( 63)= 1.0, obs( 63)= 0.262,
  iprot( 64)= 76, wt( 64)= 1.0, obs( 64)= 0.245,
  iprot( 65)= 267, wt( 65)= 1.0, obs( 65)= 0.147,
  iprot( 66)= 188, wt( 66)= 1.0, obs( 66)= 0.503,
  iprot( 67)= 164, wt( 67)= 1.0, obs( 67)= 0.544,
  iprot( 68)= 220, wt( 68)= 1.0, obs( 68)= 0.332,
  iprot( 69)= 196, wt( 69)= 1.0, obs( 69)= 0.625,
  iprot( 70)= 489, wt( 70)= 1.0, obs( 70)= -0.336,
  iprot( 71)= 521, wt( 71)= 1.0, obs( 71)= -0.497,
  iprot( 72)= 300, wt( 72)= 1.0, obs( 72)= -0.367,
  iprot( 73)= 362, wt( 73)= 1.0, obs( 73)= -0.384,
  iprot( 74)= 553, wt( 74)= 1.0, obs( 74)= -0.644,
  iprot( 75)= 616, wt( 75)= 1.0, obs( 75)= -0.367,
  iprot( 76)= 189, wt( 76)= 1.0, obs( 76)= 0.715,
  iprot( 77)= 165, wt( 77)= 1.0, obs( 77)= 0.374,
  iprot( 78)= 221, wt( 78)= 1.0, obs( 78)= 0.617,
  iprot( 79)= 197, wt( 79)= 1.0, obs( 79)= 0.505,
  iprot( 80)= 59, wt( 80)= 1.0, obs( 80)= -0.079,
  iprot( 81)= 37, wt( 81)= 1.0, obs( 81)= 0.539,
  iprot( 82)= 250, wt( 82)= 1.0, obs( 82)= -0.409,
  iprot( 83)= 228, wt( 83)= 1.0, obs( 83)= 0.627,
  iprot( 84)= 106, wt( 84)= 1.0, obs( 84)= 0.765,
  iprot( 85)= 122, wt( 85)= 1.0, obs( 85)= 0.489,
  iprot( 86)= 103, wt( 86)= 1.0, obs( 86)= 0.231,
  iprot( 87)= 138, wt( 87)= 1.0, obs( 87)= 0.438,
  iprot( 88)= 154, wt( 88)= 1.0, obs( 88)= 0.512,
  iprot( 89)= 135, wt( 89)= 1.0, obs( 89)= 0.101,
  iprot( 90)= 60, wt( 90)= 1.0, obs( 90)= 0.312,
  iprot( 91)= 38, wt( 91)= 1.0, obs( 91)= 0.419,
  iprot( 92)= 251, wt( 92)= 1.0, obs( 92)= 0.088,
  iprot( 93)= 229, wt( 93)= 1.0, obs( 93)= 0.378,
  iprot( 94)= 29, wt( 94)= 1.0, obs( 94)= 0.368,
  iprot( 95)= 4, wt( 95)= 1.0, obs( 95)= 0.115,
  iprot( 96)= 92, wt( 96)= 1.0, obs( 96)= 0.433,
  iprot( 97)= 67, wt( 97)= 1.0, obs( 97)= 0.551,
  iprot( 98)= 283, wt( 98)= 1.0, obs( 98)= 0.340,
  iprot( 99)= 258, wt( 99)= 1.0, obs( 99)= 0.413,
  iprot( 100)= 329, wt( 100)= 1.0, obs( 100)= 0.262,
  iprot( 101)= 392, wt( 101)= 1.0, obs( 101)= 0.245,
  iprot( 102)= 583, wt( 102)= 1.0, obs( 102)= 0.147,
  iprot( 103)= 504, wt( 103)= 1.0, obs( 103)= 0.503,
  iprot( 104)= 480, wt( 104)= 1.0, obs( 104)= 0.544,
  iprot( 105)= 536, wt( 105)= 1.0, obs( 105)= 0.332,
  iprot( 106)= 512, wt( 106)= 1.0, obs( 106)= 0.625,
  iprot( 107)= 30, wt( 107)= 1.0, obs( 107)= 0.627,
  iprot( 108)= 5, wt( 108)= 1.0, obs( 108)= -0.005,
  iprot( 109)= 93, wt( 109)= 1.0, obs( 109)= 0.658,
  iprot( 110)= 68, wt( 110)= 1.0, obs( 110)= 0.371,
  iprot( 111)= 284, wt( 111)= 1.0, obs( 111)= 0.536,
  iprot( 112)= 259, wt( 112)= 1.0, obs( 112)= 0.371,
  iprot( 113)= 505, wt( 113)= 1.0, obs( 113)= 0.715,
  iprot( 114)= 481, wt( 114)= 1.0, obs( 114)= 0.374,
  iprot( 115)= 537, wt( 115)= 1.0, obs( 115)= 0.617,
  iprot( 116)= 513, wt( 116)= 1.0, obs( 116)= 0.505,
  iprot( 117)= 313, wt( 117)= 1.0, obs( 117)= -0.057,
  iprot( 118)= 291, wt( 118)= 1.0, obs( 118)= 0.442,
  iprot( 119)= 375, wt( 119)= 1.0, obs( 119)= -0.079,
  iprot( 120)= 353, wt( 120)= 1.0, obs( 120)= 0.539,
  iprot( 121)= 566, wt( 121)= 1.0, obs( 121)= -0.409,
  iprot( 122)= 544, wt( 122)= 1.0, obs( 122)= 0.627,
  iprot( 123)= 629, wt( 123)= 1.0, obs( 123)= -0.057,
  iprot( 124)= 607, wt( 124)= 1.0, obs( 124)= 0.442,
  iprot( 125)= 422, wt( 125)= 1.0, obs( 125)= 0.765,
  iprot( 126)= 438, wt( 126)= 1.0, obs( 126)= 0.489,
  iprot( 127)= 419, wt( 127)= 1.0, obs( 127)= 0.231,
  iprot( 128)= 454, wt( 128)= 1.0, obs( 128)= 0.438,
  iprot( 129)= 470, wt( 129)= 1.0, obs( 129)= 0.512,
  iprot( 130)= 451, wt( 130)= 1.0, obs( 130)= 0.101,
  iprot( 131)= 314, wt( 131)= 1.0, obs( 131)= 0.013,
  iprot( 132)= 292, wt( 132)= 1.0, obs( 132)= 0.506,
  iprot( 133)= 376, wt( 133)= 1.0, obs( 133)= 0.312,
  iprot( 134)= 354, wt( 134)= 1.0, obs( 134)= 0.419,
  iprot( 135)= 567, wt( 135)= 1.0, obs( 135)= 0.088,
  iprot( 136)= 545, wt( 136)= 1.0, obs( 136)= 0.378,
  iprot( 137)= 630, wt( 137)= 1.0, obs( 137)= 0.013,
  iprot( 138)= 608, wt( 138)= 1.0, obs( 138)= 0.506,
  iprot( 139)= 109, wt( 139)= 1.0, obs( 139)= -0.203,
  iprot( 140)= 141, wt( 140)= 1.0, obs( 140)= -0.111,
  iprot( 141)= 345, wt( 141)= 1.0, obs( 141)= 0.368,
  iprot( 142)= 320, wt( 142)= 1.0, obs( 142)= 0.115,
  iprot( 143)= 408, wt( 143)= 1.0, obs( 143)= 0.433,
  iprot( 144)= 383, wt( 144)= 1.0, obs( 144)= 0.551,
  iprot( 145)= 599, wt( 145)= 1.0, obs( 145)= 0.340,
  iprot( 146)= 574, wt( 146)= 1.0, obs( 146)= 0.413,
  iprot( 147)= 346, wt( 147)= 1.0, obs( 147)= 0.627,
  iprot( 148)= 321, wt( 148)= 1.0, obs( 148)= -0.005,
  iprot( 149)= 409, wt( 149)= 1.0, obs( 149)= 0.658,
  iprot( 150)= 384, wt( 150)= 1.0, obs( 150)= 0.371,
  iprot( 151)= 600, wt( 151)= 1.0, obs( 151)= 0.536,
  iprot( 152)= 575, wt( 152)= 1.0, obs( 152)= 0.371,
  iprot( 153)= 112, wt( 153)=-1.0,
  iprot( 154)= 113, wt( 154)=-1.0,
  iprot( 155)= 114, wt( 155)= 1.0, obs( 155)= -0.434,
  iprot( 156)= 144, wt( 156)=-1.0,
  iprot( 157)= 145, wt( 157)=-1.0,
  iprot( 158)= 146, wt( 158)= 1.0, obs( 158)= -0.212,
  iprot( 159)= 425, wt( 159)= 1.0, obs( 159)= -0.203,
  iprot( 160)= 457, wt( 160)= 1.0, obs( 160)= -0.111,
  iprot( 161)= 124, wt( 161)= 1.0, obs( 161)= -0.197,
  iprot( 162)= 100, wt( 162)= 1.0, obs( 162)= 0.691,
  iprot( 163)= 156, wt( 163)= 1.0, obs( 163)= -0.230,
  iprot( 164)= 132, wt( 164)= 1.0, obs( 164)= 0.533,
  iprot( 165)= 125, wt( 165)= 1.0, obs( 165)= 0.361,
  iprot( 166)= 101, wt( 166)= 1.0, obs( 166)= 0.448,
  iprot( 167)= 157, wt( 167)= 1.0, obs( 167)= 0.211,
  iprot( 168)= 133, wt( 168)= 1.0, obs( 168)= 0.413,
  iprot( 169)= 428, wt( 169)=-1.0,
  iprot( 170)= 429, wt( 170)=-1.0,
  iprot( 171)= 430, wt( 171)= 1.0, obs( 171)= -0.434,
  iprot( 172)= 460, wt( 172)=-1.0,
  iprot( 173)= 461, wt( 173)=-1.0,
  iprot( 174)= 462, wt( 174)= 1.0, obs( 174)= -0.212,
  iprot( 175)= 440, wt( 175)= 1.0, obs( 175)= -0.197,
  iprot( 176)= 416, wt( 176)= 1.0, obs( 176)= 0.691,
  iprot( 177)= 472, wt( 177)= 1.0, obs( 177)= -0.230,
  iprot( 178)= 448, wt( 178)= 1.0, obs( 178)= 0.533,
  iprot( 179)= 441, wt( 179)= 1.0, obs( 179)= 0.361,
  iprot( 180)= 417, wt( 180)= 1.0, obs( 180)= 0.448,
  iprot( 181)= 473, wt( 181)= 1.0, obs( 181)= 0.211,
  iprot( 182)= 449, wt( 182)= 1.0, obs( 182)= 0.413,
  nprot = 182, nter=0,
 &end
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