What is the goal of this simulation? Do you have expected outcomes? Also,
why did you select this gb model? Are you following a published protocol
for work that had similar goals?
On Apr 2, 2013 7:36 AM, "Kamakshi" <kamakshi87.gmail.com> wrote:
> Dear amber users
>
> I am trying to simulate a* 37* residue long *peptide u*sing *GB-OBC
> *approximation.
>
>
> The simulation was carried out in 3 steps-
> 1. Minimization
> 2. Heating for 1 ns from 0 to 300 K
> 3. Production run for 30 ns.
>
> The inputs for the same are given below:
>
> *minimization
> &cntrl*
> imin=1, maxcyc=100,
> cut=300.0, igb=2, saltcon=0.2, gbsa=1,
> ntpr=10, ntx=1, ntb=0,
> &end
> /
>
> *Stage 1 heating of cath 0 to 300K
> &cntrl*
> imin=0, irest=0, ntx=1,
> nstlim=500000, dt=0.002,
> ntc=2, ntf=2,
> ntt=3, tautp=1.0, gamma_ln=1,
> tempi=0.0, temp0=300.0,
> ntpr=500, ntwx=500,
> ntb=0, igb=2, cut=12,
> /
>
> *Stage 2 md of cath at 30ns
> &cntr**l*
> imin=0, irest=1, ntx=5,
> nstlim=15000000, dt=0.002,
> ntc=2, ntf=2,
> ntt=3, tautp=1.0, gamma_ln=1,
> tempi=300.0, temp0=300.0,
> ntpr=500, ntwx=500, ntwe=500, nscm=1000,
> ntb=0, igb=2, saltcon=0.2, gbsa=1, cut=12,
> /
> ~
>
> Although the potential, total, kinetic energies, temperature when were
> plotted using xmgrace, the trajectory seemed to be stable. But when the
> dihedrals were calculated using ptraj and were plotted using xmgrace, the
> plot wasn't as expected( attached png of one dihedral angle)
>
> When the trajectory was viewed in VMD no secondary structure is getting
> attained, a *random coil* structure being shown.
>
> Can u please help us. if some important* input paramete*r we might be
> missing.
>
> In anticipation of getting a solution from you soon.
>
> Thanking you
> Sincerely Your's
> Kamakshi
>
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Received on Tue Apr 02 2013 - 05:00:04 PDT
