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
Received on Fri Jul 19 2002 - 08:18:53 PDT
