Dear all,
I am trying to run MD simulations using residual dipolar coupling (RDC) as restraints in explicit water (see bellow the input and the RDC files). I use as starting “inpcrd” file a structure previously equilibrated in water at 300K.
I would like to know if this protocol is correct. When I run the MD simulations, sander reads the file with the restraints (file rdcOpennew.txt, see bellow) but it says: “** No restraint defined **”.
I have seen in the example provided by AMBER ($AMBERHOME/test/rdc) that an extra file (RST.csa) is added in the restraint section. The authors say that the “csa” restraints are dummies, intended to match the RDC values.
On the other hand, is it necessary to kill the translational and rotational motion of the center-of-mass to keep the molecule aligned?
Thank you very much in advance.
Francisco
——————
INPUT File
——————
10 ns production
&cntrl
imin = 0,
irest = 1,
nmropt = 2,
ntx = 7,
ntb = 1,
cut = 8.0,
ntr = 0,
ntc = 1,
ntf = 1,
tempi = 300.0,
temp0 = 300.0,
ntt = 2,
iscale = 5,
nscm = 10
nstlim = 10000000, dt = 0.001,
ntpr = 1000, ntwx = 1000, ntwr = 1000,
/
#
&wt type='REST', istep1=0,istep2=10000,value1=0.1,
value2=1.0, /
&wt type='END' /
LISTOUT=POUT
DIPOLE=rdcOpennew.txt
———————————————————————
RDC restraint file: rdcOpennew.txt
———————————————————————
&align
ndip=35, dcut=-1.0, dwt=35*0.1,
gigj = 35*-3.163,
s11=-26.511, s22=18.714, s12=4.242, s13=18.271, s23=-3.046,
id(1)=2124, jd(1)=2125, dobsl(1)= 6.40, dobsu(1)= 6.40,
id(2)=653, jd(2)=654, dobsl(2)= -8.33, dobsu(2)= -8.33,
id(3)=3653, jd(3)=3654, dobsl(3)= -11.90, dobsu(3)= -11.90,
id(4)=1939, jd(4)=1940, dobsl(4)= 4.17, dobsu(4)= 4.17,
id(5)=1699, jd(5)=1700, dobsl(5)= 11.90, dobsu(5)= 11.90,
id(6)=2579, jd(6)=2580, dobsl(6)= 4.76, dobsu(6)= 4.76,
id(7)=1341, jd(7)=1342, dobsl(7)= 9.50, dobsu(7)= 9.50,
id(8)=679, jd(8)=680, dobsl(8)= 0.00, dobsu(8)= 0.00,
id(9)=132, jd(9)=133, dobsl(9)= 1.22, dobsu(9)= 1.22,
id(10)=3858, jd(10)=3859, dobsl(10)= -1.20, dobsu(10)= -1.20,
id(11)=980, jd(11)=981, dobsl(11)= 3.57, dobsu(11)= 3.57,
id(12)=4514, jd(12)=4515, dobsl(12)= 5.01, dobsu(12)= 5.01,
id(13)=1325, jd(13)=1326, dobsl(13)= 5.90, dobsu(13)= 5.90,
id(14)=83, jd(14)=84, dobsl(14)= 0.95, dobsu(14)= 0.95,
id(15)=4279, jd(15)=4280, dobsl(15)= 4.76, dobsu(15)= 4.76,
id(16)=3891, jd(16)=3892, dobsl(16)= 1.78, dobsu(16)= 1.78,
id(17)=544, jd(17)=545, dobsl(17)= 6.10, dobsu(17)= 6.10,
id(18)=2167, jd(18)=2168, dobsl(18)= 2.03, dobsu(18)= 2.03,
id(19)=3903, jd(19)=3904, dobsl(19)= 0.00, dobsu(19)= 0.00,
id(20)=1009, jd(20)=1010, dobsl(20)= 3.50, dobsu(20)= 3.50,
id(21)=563, jd(21)=564, dobsl(21)= 1.20, dobsu(21)= 1.20,
id(22)=2690, jd(22)=2691, dobsl(22)= 10.00, dobsu(22)= 10.00,
id(23)=1610, jd(23)=1611, dobsl(23)= 9.50, dobsu(23)= 9.50,
id(24)=3828, jd(24)=3829, dobsl(24)= -3.00, dobsu(24)= -3.00,
id(25)=1217, jd(25)=1218, dobsl(25)= 5.95, dobsu(25)= 5.95,
id(26)=1641, jd(26)=1642, dobsl(26)= 10.70, dobsu(26)= 10.70,
id(27)=2675, jd(27)=2676, dobsl(27)= 2.44, dobsu(27)= 2.44,
id(28)=3582, jd(28)=3583, dobsl(28)= -1.80, dobsu(28)= -1.80,
id(29)=4346, jd(29)=4347, dobsl(29)= 9.16, dobsu(29)= 9.16,
id(30)=1678, jd(30)=1679, dobsl(30)= 9.55, dobsu(30)= 9.55,
id(31)=1685, jd(31)=1686, dobsl(31)= 11.90, dobsu(31)= 11.90,
id(32)=3506, jd(32)=3507, dobsl(32)= 1.00, dobsu(32)= 1.00,
id(33)=4208, jd(33)=4209, dobsl(33)= 4.52, dobsu(33)= 4.52,
id(34)=4140, jd(34)=4141, dobsl(34)= 2.38, dobsu(34)= 2.38,
id(35)=1241, jd(35)=1242, dobsl(35)= 5.95, dobsu(35)= 5.95,
/
—
Francisco Corzana
Departamento de Química
Complejo Científico-Tecnológico
Universidad de La Rioja
Madre de Dios, 51.
26006 Logroño (La Rioja) Spain
e-mail: francisco.corzana.unirioja.es<mailto:francisco.corzana.unirioja.es>
www.francisco-corzana.com<
http://www.francisco-corzana.com>
Tel +34941299632
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Received on Fri Apr 01 2016 - 00:00:03 PDT
