Re: AMBER:a question about RMSD

From: Carlos Simmerling <>
Date: Tue, 24 Apr 2007 09:06:40 -0400

I am copying this to the Amber email reflector, since that is where you should
send these questions.

I do not think the difference comes frmo the programs, RMSD is pretty well
defined and you should get very similar values with different programs.
In this case you have some values saying that the structures differ a lot
(3A or more) and some saying they are nearly identical (under 1A).
You should be able to tell the difference between these two visually.
Probably you do not use the same atom selection, or the same reference
structure, or perhaps one does a best-fit and the other does not. Without
seeing your inputs I cannot really help any more than that.
It also seems unlikely that the RMSD for C atoms is much bigger than
for N or CA- they are on the same chain.

On 4/24/07, <> wrote:
> Dear Mr.Carlos:
> We use ptraj/carnal to calculate RMSD between a simulated structure and a
> NMR structure, and the backbone rmsd is 3.37 angstroms,but when we use
> chimera or VMD, we find the backbone rmsd is 0.686 and 0.729 angstroms,
> respectively.
> We found that the .C atoms'big rmsd lead to large RMSD among main chain RMSD
> (.C,CA,N). We have following problems here:
> 1. Why we acquire different value through different method? Personally I
> think the differences are due to the algorithm.
> 2. Why the value calculated by ptraj differ so much compared with other two
> methods especially for main chain .C atoms?
> Many thanks in advance!
> zehan
> ________________________________
> 免费试玩2006中国最佳网络游戏--梦幻西游

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Received on Wed Apr 25 2007 - 06:07:34 PDT
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