AMBER Archive (2009)

Subject: Re: [AMBER] Steps for NMR structure minimization

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Jul 01 2009 - 07:48:13 CDT

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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