yes, nd dis is nt for d frst tme m running sander, i hd carried out
simulations of 3 DNA sequences as well one drug molecule using sander, in
all said cases it wrkd fine.
bt while running simulated annealing its gvng prblm, rather its nt at all
gvng ny error, wn i gv d command smply command prompt appears.
i doubt whthr my input file is correct or "anneal.in"
On 4/11/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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
> > > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> > >
> >
> >
> >
> > --
> >
> > Anju Sharma
> > Project Fellow,
> > NIT, Hamirpur (H.P.)
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
--
Anju Sharma
Project Fellow,
NIT, Hamirpur (H.P.)
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Received on Sun Apr 15 2007 - 06:07:05 PDT
