<html>
Derrick,<br><br>
<blockquote type=cite class=cite cite>thank you for the information, a
quick question about it. tbere would be<br>
no problem with removing the water molecules added by genbox, but how do
i<br>
add the water molecules? and is there any way to control how many
are<br>
added? thanks again.</blockquote><br>
With genbox you can specify now many molecules are added using the
"-nmol" switch, and don't use "-cs", but
"-ci" for the water molecule But they will be spread
throughout the entire box, except where other molecules are
located. So you probably have to add more than you actually want in
there, depending on the ratio in the box volume above and below the
monolayer i.e. if it was dead center then adding double the number of
water molecules should approximately put the right number below
it.<br><br>
Or, you would need to write a script that adds them yourself. I
haven't done this myself, but a colleague here has written one that
inserts molecules randomly into a given box (the random molecule engine
with genbox has some problems). Wouldn't be too much of an issue to
add constraints on the region within the box to place them You
would just have to specify the coordinate file to insert them into, the
coordinate file for the water molecule, how many to insert, and the
allowable regions of the box i.e. where the "bottom" of the
monolayer is located. How you do this code wise, well, best idea I
suppose is look at the coding for genbox.<br><br>
Hope this helps.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
<font face="Times New Roman, Times">--------------------------------------------------------------------------<br>
<i>When the only tool you own is a hammer, every problem begins to
resemble a nail.</font></i></html>