On Mon, Jun 29, 2009, Prem Prakash Pathak wrote:
> Dear All, i wanted to minimize my NMR structure of protein of 15 kDa using
> AMBER9
>
> i have followed, following steps. is it right
>
> Hold the adf fixed
> 500.0
This is way to strong a restraint. Consider using a value at least 100 times
smaller.
> ntr = 0, ((((((( putting ntr=0 Ok.)))) ntr=1 gives problem here i do
> not know why
You don't give any error message, but it looks like you did not include the
group input required when ntr=1.
> cut = 12,
This is way too big for a solvated, periodic simulation; use the default of 8.
> step 4. MD run for 5ps
Run as long as you can. Presumably(?) you have already done a gas-phase or
implicit solvent refinement using simulated annealing. Solvated refinement
should only be a final step, since you won't explore all that much
conformational space.
...dac
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Received on Mon Jul 06 2009 - 12:27:18 PDT
