On Mon, Nov 07, 2011, hai wei wrote:
>
> 2. Heating the system to 360K:
> &cntrl
> imin = 0, irest = 0, ntx = 1, ntp = 0, ntb = 1,
> cut = 10,
> ibelly = 1,
> ntc = 2, ntf = 2, tempi = 0.0, temp0 = 360.0,
> ntt = 2, (ibelly does not work with ntt=3,)
> gamma_ln = 1.0, nstlim = 10000, dt = 0.002, ntpr = 250, ntwx = 250,
> ntwr = 10000,
> iwrap = 1, ioutfm=1, nscm = 100, /
>
> Keep protein and Graphen sheet fiexed with ibelly
> RES 1 605
> END
> END
This is wrong: with belly, the group specification is for the atoms you want
to be allowed to move, not the ones you want to keep fixed. (This is
"backwards" from the ntr=1 restraints). So the code you have above allows
residues 1 to 605 to move, and keeps the waters fixed. This is almost
certainly not what you want.
My recommendation is to avoid using belly, and just use ntr=1 restraints.
...dac
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Received on Mon Nov 07 2011 - 06:30:03 PST
