Periodic water box

From: Rudesh Toofanny <>
Date: Fri 14 Jun 2002 13:41:01 +0100


I have a problem which I have encountered in AMBER 5,6 and 7. I have two
helices in water both the same aa seqeunce but aligned antiparallel to
one another, the helices are not connect but can be considered 2
separate proteins. I have surrounded the proteins with a waterbox in
Xleap. I have then minimized the proteins in water for 100000 steps. I
have then tried to heat up the water from 0 -298K over 100000steps and
then let it equilbrate over a further 100000steps. As far as I know I
have set up a periodic box , however looking at the structure after
these 200000 steps it appears as if the water is in a diamond shape..i.e
not adhering to the Periodic box at all. In the out put file EWALD seems
to set up a box which is close to values that Xleap gave for the box but
not exactly the same.I have tried both constant pressure and
volume...but still no joy can anyone help me!

Here is the input file for the heating up and equilibration under
constant pressure:
   irest=0, ibelly=1, ntx=1, tempi=0.0, ntb=2,
   ntt=1, temp0=298.0, tautp=0.1, ntp=0, nstlim=200000,
   dt=0.001, ntc=2, ntf=2, scee=1.2, cut=10,
   nsnb=2000, ntpr=200, ntwx=2000, nmropt=1, ntp=1,

 &wt type='TEMP0', istep1=0, istep2=100000, value1=0.0, value2=298.0,
 &wt type='END', &end
 &rst iat=0, &end
-belly = water residues only
RES 85 7246



Rudesh Toofanny
EPSRC PhD Student
Laboratory of Biophysics and Surface Analysis
The Boots Science Building
School of Pharmaceutical Sciences
University of Nottingham NG7 2RD
tel: +44 (0)115 9566272
fax: +44 (0)115 9515110
Received on Fri Jun 14 2002 - 05:41:01 PDT
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