AMBER Archive (2004)

Subject: Re: AMBER: ptraj questions

From: Carlos Simmerling (
Date: Sun Oct 31 2004 - 09:45:21 CST

I think nofit is broken, so overlap of 1 residue will always be small.

>The numbers I get are too small (around 0.05). The rmsd of CA is about
>1.2. So I suppose the rmsd of this sidechain should be around this
>number or larger.

you cannot mathematically define an overlap for less than 3 atoms.

>Another problem I have is when I choose less than three atoms of the
>sidechain, the program fails.
>Thanks for your help in advance.
>By the way, the ptraj program I have is ptraj-6.5.
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