AMBER Archive (2002)

Subject: Re: solvatebox

From: Luis Gracia (luis.gracia_at_mssm.edu)
Date: Wed Dec 18 2002 - 09:58:47 CST

Luis Gracia wrote:
> hi everybody!
>
> Does the solvateBox command in LEaP (amber 6) orient the solute molecule
> before adding the waters? I thought it shouldn't do it as it says in the
> manual to use alignAxes to do it, but it seems to me that it actually
> orients the solute (well, xleap clear shows that re-orientation
> graphically). Is there a way to avoid this orientation?
>
> Thanks a lot and happy holidays to everybody.
>
> Kind regards, Luis

I just figure out what happens: I used solvatebox with the 'iso' keyword
, which automatically reorients the solute. Without the 'iso' keyword no
reorientation is made.

Kind regards, Luis 

-- 
Luis Gracia, PhD
Dept. Physiology & Biophysics, 21-280
Mt Sinai School of Medicine
One Gustave L. Levy Place, New York NY 10029
Tel: (212) 241-0858   ---   Fax: (212) 860-3369
e.mail: luis.gracia_at_mssm.edu