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: siriwong_at_theochem.tu-muenchen.de
[mailto:siriwong_at_theochem.tu-muenchen.de]
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 - 07:42:38 PST
