Re: Average structure

From: Laurent Chiche <>
Date: Thu 29 Mar 2001 18:01:32 +0200

Of course CARNAL can also compute average structures... but does not
solve the distorsion.
One alternative to minimized average structure is to
-first calculate the average structure
-then choose among the snapshots the conformation closest to the average
BTW 20 is not much!
In this way you get a close to average real structure.

Guanglei Cui a écrit :
> I think MoilView by Carlos Simmerling and ptraj by Tom Cheatham both can
> generate average structures from dynamics. However, the averaged structure
> can be distorted, especially when there's large conformational change such
> as terminal base pair opening. I've seen the ring of one terminal base
> shrinked significantly. Minimization doesn't help to correct this as far as
> I know. Good luck!
> Guanglei Cui
> Dept. of Chemistry
> SUNY at Stony Brook
> Stony Brook, NY 11790
> -----Original Message-----
> From:
> []
> Sent: Thursday, March 29, 2001 10:07 AM
> To: amber
> Subject: Average structure
> Dear All,
> Could anyone suggest me to calculate average coordinate of DNA in
> trajectoty file? I have 20 snapshots in trajectory and I would like to
> investigate average structure.
> Thanks in adavnce,
> Khatcharin
Received on Thu Mar 29 2001 - 08:01:32 PST
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