Hi, All,
Do you notice the difference of Amber ff03 force field between Amber8 and
Amber10 for dipeptide ACE-ALA-NME? I found the charges of atoms from ACE and
NME terminals are different in Amber8 ff03 and Amber10 ff03 force fields but
the charges of atoms from ALA unit are same. The detailed charges for all
atoms in Ala2 dipeptide are shown as follows:
For Amber8 ff03 force field:
%FLAG CHARGE
%FORMAT(5E16.8)
2.04636429E+00 -6.67300626E+00 2.04636429E+00 2.04636429E+00
1.08823576E+01
-1.03484442E+01 -7.37589504E+00 5.36238555E+00 -5.05359046E-01
2.20129028E+00
-4.19023611E+00 1.41091624E+00 1.41091624E+00 1.41091624E+00
1.03907928E+01
-1.01157272E+01 -7.57501011E+00 4.95464337E+00 -2.71512270E+00
1.77849648E+00
1.77849648E+00 1.77849648E+00
For Amber10 ff03 force field:
%FLAG CHARGE
%FORMAT(5E16.8)
1.38507702E+00 -3.46702946E+00 1.38507702E+00 1.38507702E+00
9.33716119E+00
-1.00253628E+01 -7.37589504E+00 5.36238555E+00 -5.05359046E-01
2.20129028E+00
-4.19023611E+00 1.41091624E+00 1.41091624E+00 1.41091624E+00
1.03907928E+01
-1.01157272E+01 -7.72421430E+00 5.28648968E+00 -9.89343334E-01
1.14235599E+00
1.14235599E+00 1.14235599E+00
Why is the ff03 force field in Amber8 and Amber10 different? Will the
difference of charges lead to important Ala2 conformation difference?
Thanks!
Dongshan
-----------------------------------------------------------------------------------
Dr. Dongshan Wei
Department of Chemistry
Boston University
Boston, MA, 02215
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Received on Thu Dec 10 2009 - 16:00:02 PST
