Hello
I am new user for Amber creating cubic water box and to creat it I go through
the AMBER9 manual.SolvateBox command creates rectangular box using buffer
argument if it is single number it add water in X, Y, Z axes respectively unless
'iso' argument is use to make box cubic.
But according to Amber mailing archive there is no need to specify 'iso' argument
http://archive.ambermd.org/200905/0275.html
According to Tutorial-1 of Begining Amber workshop (Simulating a small fragment
of DNA)
list of number specifying in SolvateBox command to make water box cubic.
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section2.htm
According to these when I tried to creat the cubic water box by specifying list
of buffer value (8.0 8.0 8.0. Leap not creating box.
solvateBox wat TIP3PBOX 8.0 8.0 8.0
Solute vdw bounding box: 3.726 3.695 3.537
Total bounding box for atom centers: 19.726 19.695 19.537
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 3.726 3.695 3.537 angstroms.
Volume: 48.683 A^3
Total mass 18.016 amu, Density 0.615 g/cc
Added 0 residues.
What is the problem, why leap not creating box.
With due regards.
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Mon Feb 08 2010 - 10:00:03 PST
