Here is a minor change in leaprc.ff03.
This change is needed since the ff03 version of ACE- and -NME terminal
groups are now given in all_amino03.lib while the same groups also exist
in all_amino(n,c)t94.lib in ff94 version. As a consequence, when
all_amino(c,n)t94.lib are loaded after all_amino03.lib, the ACE- and
-NME groups of ff94 version (with Cornell et al charges) are loaded.
This does not affect simulation of proteins but can adversely affect the
results of small peptides (e.g., Ace-Ala-Nme).
A remedy is to move the line "loadOff all_amino03.lib" after "loadOff
all_aminoct94.lib" and "loadOff all_aminont94.lib".
Let me know if you have any questions.
yong
*************************************************
*** amber8/dat/leap/cmd/leaprc.ff03.old2 2004-01-16
02:02:21.000000000 -0500
--- amber8/dat/leap/cmd/leaprc.ff03 2004-06-01 15:32:00.000000000
-0400
***************
*** 88,97 ****
frcmod03 = loadamberparams frcmod.ff03
#
- # Load amino acid libraries.
- #
- loadOff all_amino03.lib
- #
# Load water and ions
#
loadOff ions94.lib
--- 88,93 ----
***************
*** 110,118 ****
--- 106,120 ----
#
# Load main chain and terminating
# amino acid libraries.
+ # These three libraries have to be loaded in this order since ACE NME
are
+ # now in all_amino03.lib
#
loadOff all_aminoct94.lib
loadOff all_aminont94.lib
+ #
+ # Load amino acid libraries.
+ #
+ loadOff all_amino03.lib
#
# Define the PDB name map for the amino acids and DNA.
Received on Wed Apr 05 2006 - 23:50:02 PDT
