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AMBER Archive (2003)Subject: Residual dipolar couplings
From: McAteer, Kathleen (Kathleen.McAteer_at_pnl.gov)
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!
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&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
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Thanks!
Kate
Kathleen McAteer
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