AMBER Archive (2003)

Subject: Residual dipolar couplings

From: McAteer, Kathleen (Kathleen.McAteer_at_pnl.gov)
Date: Tue May 20 2003 - 16:03:58 CDT

First, I apologise for the length of this message. I was wondering if anyone could help me find the problem I am having when I use RDCs in a DNA simulation in AMBER7. I run into a vlimit error after 11 psec of MD and my final energies are huge! The total distance penalty is 30000 and the total align constraint is 127. If I use the same starting structure and restraint files with AMBER6 I get a reasonable final structure and low energies. I am including both input files and the restraint file for RDCs used with both programs.

AMBER6

simulated annealing protocol, 20 ps at 300 K &cntrl nstlim=20000, pencut=0, nmropt=2, ntpr=1000, ntt=1, ntwx=1000, iscale=5, cut=15.0, ntb=0, igb=3, vlimit=20, &end &ewald eedmeth=5 &end # #Simple simulated annealing algorithm: # #from steps 0 to 20000: restrained MD at 300 K# &wt type='TEMP0', istep1=0,istep2=20000,value1=300., value2=300., &end &wt type='TAUTP', is!
tep1=0,istep2=1000,value1=0.4, value2=0.4, &end &wt type='TAUTP', istep1=1001,istep2=20000,value1=4.0, value2=4.0, &end &wt type='REST', istep1=0,istep2=5000,value1=0.1, value2=1.0, &end &wt type='REST', istep1=5001,istep2=20000,value1=1.0, value2=1.0, &end &wt type='END' &endLISTOUT=POUT DISANG=RST.dick2DIPOLE=RST_nh.dip

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RST_nh.dip

&align ndip=12, dcut=-1.0, fj=0.1, dfac_al=12*-0.21341, s11=-10, s22=-10, 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

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AMBER7
 simulated annealing protocol, 20 ps at 300 K &cntrl nstlim=20000, pencut=0, nmropt=2, ntpr=1000, ntt=1, ntwx=1000, iscale=5, cut=15.0, ntb=0, vlimit=20, &end &ewald eedmeth=5 &end # #Simple simulated annealing algorithm: # #from steps 0 to 20000: restrained MD at 300 K# &wt type='TEMP0', istep1=0,istep2=20000,value1=300., value2=300., &end &wt type='TAUTP', istep1=0!
,istep2=1000,value1=0.4, value2=0.4, &end &wt type='TAUTP', istep1=1001,istep2=20000,value1=4.0, value2=4.0, &end &wt type='REST', istep1=0,istep2=5000,value1=0.1, value2=1.0, &end &wt type='REST', istep1=5001,istep2=20000,value1=1.0, value2=1.0, &end &wt type='END' &endLISTOUT=POUT DISANG=RST.dick2DIPOLE=RST_nh2.dip

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RST_nh2.dip
 &align ndip=12, dcut=-1.0, gigj=12*-3.163, dij=12*1.01, dwt=12*0.1, s11=-10, s22=-10, 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

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Thanks!

Kate

Kathleen McAteer
Pacific Northwest National Laboratory
Richland, WA 99352
(509)373-5148

kathleen.mcateer_at_pnl.gov