did you run sander the same way as it was set up for the test
cases? it seems strange that the tests run fine but your own input doesn't
even start sander.
On 4/11/07, Anju Sharma <anju.020384.gmail.com> wrote:
> test cases?
> u mean the tests tht are to be runned aftr compilation.... thn yes.
>
>
> On 4/11/07, Carlos Simmerling <carlos.simmerling.gmail.com > wrote:
> >
> > did all of the test cases pass?
> >
> > On 4/11/07, Anju Sharma < anju.020384.gmail.com> wrote:
> > > Hi,
> > >
> > > 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
> > >
> > >
> > > &cntrl
> > >
> > > nstlim=20000, pencut=-0.001 , nmropt=1,
> > > ntpr=200, ntt=1, ntwx=200,
> > > cut=15.0, ntb=0, vlimit=10,
> > > /
> > >
> > > &ewald
> > > eedmeth=5,
> > > /
> > > &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 anneal.in -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.)
> >
> -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
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> >
>
>
>
> --
>
> Anju Sharma
> Project Fellow,
> NIT, Hamirpur (H.P.)
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Received on Sun Apr 15 2007 - 06:07:05 PDT
