Dear Amber users,
I want to define a parallelepiped box with specific dimensions. After
reading the numerous posts in the mailing list and the manual, I couldn't
figure out the way to create a solvated box with the desired dimensions.
The closer I could get was when I used the following commands in tleap:
mol = loadpdb protein.pdb
addIons2 mol Na+ 90 Cl- 110
solvateBox mol TIP4PEWBOX { 40 40 40 }
setBox mol vdw
set mol box { 56 108 104 }
savePDB mol protein.amber.pdb
saveAmberParm mol protein.prmtop protein.inpcrd
Although the last line of protein.inpcrd contains the right box dimensions,
the total number of atoms is ~300K whereas the box I want contains just 82K
atoms. How can I achieve that?
thanks,
Thomas
--
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Fri Dec 14 2012 - 15:30:02 PST
