Re: [AMBER] problem during MD process

From: case <>
Date: Sun, 12 Dec 2010 22:53:05 -0500

On Sun, Dec 12, 2010, 蒋峻峰 wrote:

> I am doing a project of acetyltransfer of ACO.
> Stilly, the rmsd of the whole structure turned larger than 2
> after 4ns simulation.

You don't say how large the structure is, or what atoms you used to compute
the rms difference. A 2 Ang. RMS change is not at all unusual, especially
for a sizeable protein, or if you are looking at all atoms. Also, if there
are floppy N- or C-terminal residues (or some floppy loop) they can have a big
effect on the computed RMS.

The best thing to do is to carefully examine the trajectory in a viewer like
Chimera or VMD. Don't concentrate on just a single number, but look to see
what is happening, both at the active site, and to the protein as a whole.
Start with seeing if the secondary struture is conserved, then look at more

...good luck...dac

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Received on Sun Dec 12 2010 - 20:00:03 PST
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