AMBER Archive (2003)

Subject: AMBER: FW: Residual dipolar couplings

From: McAteer, Kathleen (Kathleen.McAteer_at_pnl.gov)
Date: Fri Sep 26 2003 - 14:44:57 CDT

> ----------
> From: McAteer, Kathleen
> Sent: Wednesday, September 24, 2003 1:12 PM
> To: 'amber_at_scripps.edu'
> Subject: Residual dipolar couplings
>
> All.
> I have been trying to implement residual dipolar coupling restraints into my AMBER 7 molecular dynamics calculations but I am not happy with the resulting distance (55.8) and alignment penalties (216.47). I think I may be implementing the rdcs incorrectly as I have been successful using them in X-PLOR and had very small restraint violations.
> My input file and rdc restraint file are shown below.
> Thanks for any help you can give me!
>
> Kate
>
> simulated annealing protocol, 20 ps
>
> &cntrl
> nstlim=20000, pencut=0.001, nmropt=2,
> temp0 = 300.0, tempi = 300.0, tautp=1.0, ntpr=100, ntt=1, ntwx=100,
> ipnlty=1, tausw=0.0, mxsub = 45, iscale=5,
> scalm=300, ntc=1, vlimit=20.,
> cut=9.0,
> &end
> &ewald
> &end
> 46.9278231 47.9662761 62.9613200 90.0000000 90.0000000 90.0000000
> 50.0000000 50.0000000 65.0000000 4 0 0 0
> 0.000004
> #
> #Simple simulated annealing algorithm:
> #
> #from steps 0 to 5000: heat the system to 300K
> #from steps 5001-18000: re-cool to low temperatures with long tautp
> #from steps 18001-20000: final cooling with short tautp
> #
> &wt type='TEMP0', istep1=0,istep2=5000,value1=300.,
> value1=300., &end
> &wt type='TEMP0', istep1=5001, istep2=18000, value1=300.0,
> value2=300.0, &end
> &wt type='TEMP0', istep1=18001, istep2=20000, value1=300.0,
> value2=300.0, &end
>
> &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
> value2=0.4, &end
> &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
> value2=4.0, &end
> &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
> value2=1.0, &end
> &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
> value2=0.05, &end
>
> &wt type='REST', istep1=0,istep2=3000,value1=0.1,
> value2=1.0, &end
> &wt type='REST', istep1=3001,istep2=20000,value1=1.0,
> value2=1.0, &end
>
> &wt type='END' &end
> LISTOUT=POUT
> DISANG=RST.dick2
> DIPOLE=RST_all.dip
>
> &align
> ndip=120, dcut=-1.0, dij=108*1.09, dij=12*1.01,
> gigj=108*7.847, 12*-3.163,dwt=120*0.03,
> s11=-48.357, s22=-47.054, s12=0.0, s13=0.0, s23=0.0,
> id(1)=147, jd(1)=148, dobs(1)= 20.44,
> id(2)=179, jd(2)=180, dobs(2)= 20.31,
> id(3)=526, jd(3)=527, dobs(3)= 20.44,
> id(4)=558, jd(4)=559, dobs(4)= 20.31,
> id(5)=12, jd(5)=13, dobs(5)= 20.40,
> id(6)=75, jd(6)=76, dobs(6)= 20.35,
> id(7)=202, jd(7)=203, dobs(7)= 19.96,
> id(8)=234, jd(8)=235, dobs(8)= 20.04,
> id(9)=266, jd(9)=267, dobs(9)= 20.16,
> id(10)=329, jd(10)=330, dobs(10)= 20.40,
> id(11)=391, jd(11)=392, dobs(11)= 20.40,
> id(12)=454, jd(12)=455, dobs(12)= 20.36, >
> id(13)=581, jd(13)=582, dobs(13)= 19.97,
> id(14)=613, jd(14)=614, dobs(14)= 20.04,
> id(15)=645, jd(15)=646, dobs(15)= 20.16,
> id(16)=708, jd(16)=709, dobs(16)= 20.40,
> id(17)=42, jd(17)=43, dobs(17)= 20.46,
> id(18)=105, jd(18)=106, dobs(18)= 20.32,
> id(19)=138, jd(19)=139, dobs(19)= 20.28,
> id(20)=170, jd(20)=171, dobs(20)= 20.15,
> id(21)=296, jd(21)=297, dobs(21)= 20.30,
> id(22)=359, jd(22)=360, dobs(22)= 20.45,
> id(23)=421, jd(23)=422, dobs(23)= 20.46,
> id(24)=484, jd(24)=485, dobs(24)= 20.32,
> id(25)=517, jd(25)=518, dobs(25)= 20.27,
> id(26)=549, jd(26)=550, dobs(26)= 20.15,
> id(27)=675, jd(27)=676, dobs(27)= 20.31,
> id(28)=738, jd(28)=739, dobs(28)= 20.46,
> id(29)=738, jd(29)=739, dobs(29)= 20.74,
> id(30)=738, jd(30)=739, dobs(30)= 20.85,
> id(31)=738, jd(31)=739, dobs(31)= 20.59,
> id(32)=738, jd(32)=739, dobs(32)= 20.74,
> id(33)=738, jd(33)=739, dobs(33)= 20.74,
> id(34)=738, jd(34)=739, dobs(34)= 20.85,
> id(35)=738, jd(35)=739, dobs(35)= 20.59,
> id(36)=738, jd(36)=739, dobs(36)= 20.74,
> id(37)=9, jd(37)=10, dobs(37)= 11.90,
> id(38)=39, jd(38)=40, dobs(38)= 12.28,
> id(39)=72, jd(39)=73, dobs(39)= 12.48,
> id(40)=102, jd(40)=103, dobs(40)= 12.36,
> id(41)=135, jd(41)=136, dobs(41)= 12.01,
> id(42)=167, jd(42)=168, dobs(42)= 11.55,
> id(43)=199, jd(43)=200, dobs(43)= 11.14,
> id(44)=231, jd(44)=232, dobs(44)= 10.96,
> id(45)=263, jd(45)=264, dobs(45)= 11.08,
> id(46)=293, jd(46)=294, dobs(46)= 11.45,
> id(47)=326, jd(47)=327, dobs(47)= 11.91,
> id(48)=356, jd(48)=357, dobs(48)= 12.30,
> id(49)=388, jd(49)=389, dobs(49)= 11.89,
> id(50)=418, jd(50)=419, dobs(50)= 12.28,
> id(51)=451, jd(51)=452, dobs(51)= 12.43,
> id(52)=481, jd(52)=482, dobs(52)= 12.34,
> id(53)=514, jd(53)=515, dobs(53)= 11.99,
> id(54)=546, jd(54)=547, dobs(54)= 11.53,
> id(55)=578, jd(55)=579, dobs(55)= 11.13,
> id(56)=610, jd(56)=611, dobs(56)= 10.95,
> id(57)=642, jd(57)=643, dobs(57)= 11.06,
> id(58)=672, jd(58)=673, dobs(58)= 11.43,
> id(59)=705, jd(59)=706, dobs(59)= 11.89,
> id(60)=735, jd(60)=736, dobs(60)= 12.28,
> id(61)=25, jd(61)=736, dobs(61)= 20.88,
> id(62)=58, jd(62)=736, dobs(62)= 20.82,
> id(63)=88, jd(63)=736, dobs(63)= 20.77,
> id(64)=121, jd(64)=736, dobs(64)= 20.76,
> id(65)=153, jd(65)=736, dobs(65)= 20.80,
> id(66)=185, jd(66)=736, dobs(66)= 20.87,
> id(67)=217, jd(67)=736, dobs(67)= 20.92,
> id(68)=249, jd(68)=736, dobs(68)= 20.95,
> id(69)=279, jd(69)=736, dobs(69)= 20.95,
> id(70)=312, jd(70)=736, dobs(70)= 20.93,
> id(71)=342, jd(71)=736, dobs(71)= 20.88,
> id(72)=375, jd(72)=736, dobs(72)= 20.82,
> id(73)=404, jd(73)=736, dobs(73)= 20.88,
> id(74)=437, jd(74)=736, dobs(74)= 20.82,
> id(75)=467, jd(75)=736, dobs(75)= 20.77,
> id(76)=500, jd(76)=736, dobs(76)= 20.76,
> id(77)=532, jd(77)=736, dobs(77)= 20.80,
> id(78)=564, jd(78)=736, dobs(78)= 20.87,
> id(79)=596, jd(79)=736, dobs(79)= 20.92,
> id(80)=628, jd(80)=736, dobs(80)= 20.95,
> id(81)=658, jd(81)=736, dobs(81)= 20.95,
> id(82)=691, jd(82)=736, dobs(82)= 20.93,
> id(83)=721, jd(83)=736, dobs(83)= 20.88,
> id(84)=754, jd(84)=736, dobs(84)= 20.82,
> id(85)=23, jd(85)=24, dobs(85)= 20.63,
> id(86)=56, jd(86)=57, dobs(86)= 20.59,
> id(87)=86, jd(87)=87, dobs(87)= 20.62,
> id(88)=119, jd(88)=120, dobs(88)= 20.70,
> id(89)=151, jd(89)=152, dobs(89)= 20.78,
> id(90)=183, jd(90)=184, dobs(90)= 20.84,
> id(91)=215, jd(91)=216, dobs(91)= 20.86, >
> id(92)=247, jd(92)=248, dobs(92)= 20.85,
> id(93)=277, jd(93)=278, dobs(93)= 20.79,
> id(94)=310, jd(94)=311, dobs(94)= 20.71,
> id(95)=340, jd(95)=341, dobs(95)= 20.63,
> id(96)=373, jd(96)=374, dobs(96)= 20.59,
> id(97)=402, jd(97)=403, dobs(97)= 20.63,
> id(98)=435, jd(98)=436, dobs(98)= 20.59,
> id(99)=465, jd(99)=466, dobs(99)= 20.62,
> id(100)=498, jd(100)=499, dobs(100)= 20.70,
> id(101)=530, jd(101)=531, dobs(101)= 20.78,
> id(102)=562, jd(102)=563, dobs(102)= 20.84,
> id(103)=594, jd(103)=595, dobs(103)= 20.86,
> id(104)=626, jd(104)=627, dobs(104)= 20.85,
> id(105)=656, jd(105)=657, dobs(105)= 20.79,
> id(106)=689, jd(106)=690, dobs(106)= 20.71,
> id(107)=719, jd(107)=720, dobs(107)= 20.63,
> id(108)=752, jd(108)=753, dobs(108)= 20.84,
> id(109)=48, jd(109)=49, dobs(109)= 9.82,
> id(110)=111, jd(110)=112, dobs(110)= 9.74,
> id(111)=302, jd(111)=303, dobs(111)= 9.80,
> id(112)=365, jd(112)=366, dobs(112)= 9.82,
> id(113)=427, jd(113)=428, dobs(113)= 9.82,
> id(114)=490, jd(114)=491, dobs(114)= 9.74,
> id(115)=681, jd(115)=682, dobs(115)= 9.80,
> id(116)=744, jd(116)=745, dobs(116)= 9.82,
> id(117)=211, jd(117)=212, dobs(117)= 9.93,
> id(118)=243, jd(118)=244, dobs(118)= 9.96,
> id(119)=590, jd(119)=591, dobs(119)= 9.55,
> id(120)=622, jd(120)=623, dobs(120)= 9.59,
> &end
>
>
>

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