AMBER: Prblm rgrdng Simulated Annealing

From: Anju Sharma <>
Date: Wed, 11 Apr 2007 15:36:08 +0530


Wht i hv done so far is prepared dna str usng nucgen nd its .prmtop nd
inpcrd files r ready in vacuum as well as in water.
Now i wnt to run Simulated annealing so prepared following input file:
simulated annealing protocol, 20 ps


    nstlim=20000, pencut=-0.001, nmropt=1,
    ntpr=200, ntt=1, ntwx=200,
    cut=15.0, ntb=0, vlimit=10,
 &wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
            value2=600., /
 &wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
            value2=100.0, /
 &wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
            value2=0.0, /

 &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
            value2=0.4, /
 &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
            value2=4.0, /
 &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
            value2=0.05, /

 &wt type='END' /

Now whn i run dis file wth command

sander -O -i -o tga_ann.out -c tga_vac.inpcrd -p tga_vac.prmtop -r
tga_vac_ann.rst -x tga_vac_ann.traj

thn dere is no error, immediately command prompt appears, bt dese output
files are nt generated

Cn u pls tell me where m wrong, is dere is ny error in ny input file.

Anju Sharma
Project Fellow,
NIT, Hamirpur (H.P.)
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Received on Sun Apr 15 2007 - 06:07:04 PDT
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