Hello
I am trying to understand the SolvateBox command from tleap. Basically, in
the leap log file there is something called
Total bounding box for atom centers: 157.379 141.515 152.369
this is generated by SolvateBox before the addition of water. While after
the addition of waters there is
Total vdw box size: 160.332 144.804 155.497 angstroms.
which is actually the box information at the end of the amber coordinate
file.
Could you please tell me what is the difference between them?
I noticed that the "Total bounding box for atom centers" values are closer
to the box dimensions created by VMD/solvate (using the same solute-box
edge and solute-water distance)
Thanks in advance.
Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 08 2014 - 04:00:02 PDT
