Re: AMBER: average struct without solvent

From: <>
Date: Mon, 21 Nov 2005 14:20:39 +0000

I can be wrong, but it seems that you are averaging the coordinates,
before you
remove translation and rotational movement! If you averege the structure at
this stage, you'll get the average position of easch atom in the box, for your
simulation, and that is not the same as an average structure!
I believe you have to rms fit a seletions of atoms (or all the atoms of your
solute) and them averaging would be possible!

Please, anyone correct me if I'm wrong!

Hope it helps!

Marco A. C. Preto
PH. D. student
FCUP - Porto

Quoting C Balasubramanian <>:

> Dear users,
> I hve run a 1.5ns simulation on a 12 mer DNA in explicit solvent with
> PBC. i wanted to calculate the average structure without (excluding)
> solvent and ions. the following is the input i gave to ptraj. I am
> getting the structure but it is highly scattered and not a proper
> one. Someone please help me on this.
> trajin mde.mdcrd
> trajin mdp1.mdcrd
> trajin mdp2.mdcrd
> average avgst.pdb pdb nowrap
> center :1-24
> image familiar
> strip :WAT
> strip :Na+
> thanks,
> Bala

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Received on Mon Nov 21 2005 - 14:53:01 PST
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