AMBER Archive (2002)

Subject: RE: correction about solvateOct

From: William Wei (william_at_phm.utoronto.ca)
Date: Fri Jul 19 2002 - 10:18:53 CDT

The following is just my understanding.

-------------------------
William Wei
Faculty of Pharmacy
19 Russell Street
Toronto, ON. M5S 2S2
Tel: 1-416-946-8469
Fax: 1-416-978-8511
Email: william_at_phm.utoronto.ca
       william.wei_at_utoronto.ca

-----Original Message-----
From: Nikolai Smolin [mailto:smolin_at_steak.chemie.uni-dortmund.de]
Sent: Friday, July 19, 2002 4:10 AM
To: amber_at_heimdal.compchem.ucsf.edu
Subject: correction about solvateOct

Dear AMBER users:

I have question about solvateOct command
in Leap and I used AMBER 6,0.
I did not understand what means 'iso' option in this command.
If I want to use in my simulation PME is it necessary to use
this option for preparation my box or not?
I tried with this option and without . And I recieved different number
atoms in my system:

alignAxes protein
solvateOct protein WATBOX216 12,0 iso 0,75 in this case 28223 atoms
in box

>> This will create a cubic box, the nearest buffer distance is 12
angstroms.

alignAxes protein
solvateOct protein WATBOX216 12,0 0,75 in this case 19748 atoms in box

>> It depends how did the programer program it. If the amber take the two
number as the x and y buffer, the z buffer take either 12 or 0.75, it is a
much small box compared to the last one. If amber took 12 as the x, y, and z
buffer, and took .75 as the closeness, it is also a small box than you
defined in last command. So before you define the box, make sure what is
your purpose, and give amber a clear idea, and use the standard input.

What I made wrong?
Or it is correct?
What way for preparation box with less number of particles perfect?

Tnaks in advance!! 

--
Dipl.-Phys. Nikolai Smolin

Physikalische Chemie I
Universitaet Dortmund
Otto-Hahn-Str. 6
44221 Dortmund
Germany

Tel:     +49 / 231 / 755 3929
Fax:     +49 / 231 / 755 3901

E-mail:  smolin_at_steak.chemie.uni-dortmund.de