AMBER Archive (2005)

Subject: AMBER: radii "leap" from which file

From: xhu1_at_memphis.edu
Date: Tue Mar 08 2005 - 13:34:48 CST

Dear Ambers,

I am using AMBER 7. I have a question about radii parameter stored in
topology file: which parameter file contains radii, such as Bondi
radii, modified Bondi radii, gbjsb or mgbjsb? The default radii are
modified Bondi radii. After I "leap" like this:

tleap -s -f leaprc.ff99
-I: Adding /usr/local/amber7/dat/leap/prep to search path.
-I: Adding /usr/local/amber7/dat/leap/lib to search path.
-I: Adding /usr/local/amber7/dat/leap/parm to search path.
-I: Adding /usr/local/amber7/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leaprc.ff99.

Welcome to LEaP!
Sourcing: /usr/local/amber7/dat/leap/cmd/leaprc.ff99
Log file: ./leap.log
Loading parameters: /usr/local/amber7/dat/leap/parm/parm99.dat
Loading library: /usr/local/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_amino94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /usr/local/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /usr/local/amber7/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber7/dat/leap/lib/solvents.lib

All the parameter should be in these loaded files, but I don't find
modified Bondi radii in parm99.dat. the radii in the parm99.dat is the
van der Waals radii, right? then where do the modifed Bondi radii come
from? Thank you very much!

All the best

Shawn Hu

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