AMBER Archive (2001)

Subject: DNA strand flying

From: Stephane (steletch_at_biomedicale.univ-paris5.fr)
Date: Thu May 10 2001 - 10:48:17 CDT

I ran a 5ns dynamic with periodic condition on a solvated DNA (10bp).
During my simulation one strand goes to a mirror box and goes back.
I think it is not so bad because of the periodic condition.
But, when i try to do the trajectory with ptraj, i can not force the
strand to stay in the major box.
I've downloaded the latest version of ptraj, but i always have the same
problem.
Can someone help me ?
Here is my prtaj script :

trajin GCCGGGTCGC_sansPt.dn300K1_c.Z 1 50
...
trajin GCCGGGTCGC_sansPt.dn300K102_c.Z 1 50
trajout GCCGGGTCGC_sansPt_norm.ptraj
center :1-20
image :1-20 bymask :1-20
image byres :WAT
strip :WAT
strip :CIP
go 

-- 
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*
Teletchea Stephane - CNRS UMR 8601
Lab. de chimie et biochimie pharmacologiques et toxicologiques
45 rue des Saints-Peres 75270 Paris cedex 06
tel : (33) - 1 42 86 20 86 - fax : (33) - 1 42 86 83 87
mel : steletch_at_biomedicale.univ-paris5.fr
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