********>Bugfix 19:
Author: Yong Duan
Date: 08/03/2004
Programs: ff03 force field
Description: The charges for the (rarely used) neutral lysine (LYN) were
just copied from the ff94 force field, instead of being
regenerated with the new charge scheme.
Fix: apply the following patch to amber8/dat/leap/prep/all_amino03.in
------------------------------------------------------------------------------
*** all_amino03.in 2003/12/31 18:04:06 1.4
--- all_amino03.in 2004/06/24 17:05:37
***************
*** 780,806 ****
1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
! 4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
! 5 H H E 4 3 2 1.010 119.800 0.000 0.27190
! 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.07206
! 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.09940
! 8 CB CT 3 6 4 3 1.525 111.100 60.000 -0.04845
! 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.03400
! 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.03400
! 11 CG CT 3 8 6 4 1.525 109.470 180.000 0.06612
! 12 HG2 HC E 11 8 6 1.090 109.500 300.000 0.01041
! 13 HG3 HC E 11 8 6 1.090 109.500 60.000 0.01041
! 14 CD CT 3 11 8 6 1.525 109.470 180.000 -0.03768
! 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.01155
! 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.01155
! 17 CE CT 3 14 11 8 1.525 109.470 180.000 0.32604
! 18 HE2 HP E 17 14 11 1.090 109.500 300.000 -0.03358
! 19 HE3 HP E 17 14 11 1.090 109.500 60.000 -0.03358
! 20 NZ N3 B 17 14 11 1.470 109.470 180.000 -1.03581
! 21 HZ2 H E 20 17 14 1.010 109.470 180.000 0.38604
! 22 HZ3 H E 20 17 14 1.010 109.470 300.000 0.38604
! 23 C C M 6 4 3 1.522 111.100 180.000 0.59730
! 24 O O E 24 6 4 1.229 120.500 0.000 -0.56790
IMPROPER
-M CA N H
--- 780,814 ----
1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
! 4 N N M 3 2 1 1.335 116.600 180.000 -0.453388
! 5 H H E 4 3 2 1.010 119.800 0.000 0.289695
! 6 CA CT M 4 3 2 1.449 121.900 180.000 -0.024500
! 7 HA H1 E 6 4 3 1.090 109.500 300.000 0.099553
! 8 CB CT 3 6 4 3 1.525 111.100 60.000 0.035478
! 9 HB2 HC E 8 6 4 1.090 109.500 300.000 0.004797
! 10 HB3 HC E 8 6 4 1.090 109.500 60.000 0.004797
! 11 CG CT 3 8 6 4 1.525 109.470 180.000 -0.019962
! 12 HG2 HC E 11 8 6 1.090 109.500 300.000 -0.015610
! 13 HG3 HC E 11 8 6 1.090 109.500 60.000 -0.015610
! 14 CD CT 3 11 8 6 1.525 109.470 180.000 0.041105
! 15 HD2 HC E 14 11 8 1.090 109.500 300.000 0.008304
! 16 HD3 HC E 14 11 8 1.090 109.500 60.000 0.008304
! 17 CE CT 3 14 11 8 1.525 109.470 180.000 0.188382
! 18 HE2 HP E 17 14 11 1.090 109.500 300.000 0.016810
! 19 HE3 HP E 17 14 11 1.090 109.500 60.000 0.016810
! 20 NZ N3 B 17 14 11 1.470 109.470 180.000 -0.894254
! 21 HZ2 H E 20 17 14 1.010 109.470 180.000 0.332053
! 22 HZ3 H E 20 17 14 1.010 109.470 300.000 0.332053
! 23 C C M 6 4 3 1.522 111.100 180.000 0.608464
! 24 O O E 24 6 4 1.229 120.500 0.000 -0.563281
!
! CHARGE
! -0.453388 0.289695 -0.024500 0.099553 0.035478
! 0.004797 0.004797 -0.019962 -0.015610 -0.015610
! 0.041105 0.008304 0.008304 0.188382 0.016810
! 0.016810 -0.894254 0.332053 0.332053 0.608464
! -0.563281
!
IMPROPER
-M CA N H
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Also, you should patch amber8/dat/leap/lib/all_amino03.lib:
------------------------------------------------------------------------------
*** all_amino03.lib 2003/07/23 22:01:01 7.3
--- all_amino03.lib 2004/06/24 17:12:15
***************
*** 2121,2147 ****
0.0 0.0 0.0
0.0 0.0 0.0
!entry.LYN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
! "N" "N" 0 1 131072 1 7 -0.415700
! "H" "H" 0 1 131072 2 1 0.271900
! "CA" "CT" 0 1 131072 3 6 -0.072060
! "HA" "H1" 0 1 131072 4 1 0.099400
! "CB" "CT" 0 1 131072 5 6 -0.048450
! "HB2" "HC" 0 1 131072 6 1 0.034000
! "HB3" "HC" 0 1 131072 7 1 0.034000
! "CG" "CT" 0 1 131072 8 6 0.066120
! "HG2" "HC" 0 1 131072 9 1 0.010410
! "HG3" "HC" 0 1 131072 10 1 0.010410
! "CD" "CT" 0 1 131072 11 6 -0.037680
! "HD2" "HC" 0 1 131072 12 1 0.011550
! "HD3" "HC" 0 1 131072 13 1 0.011550
! "CE" "CT" 0 1 131072 14 6 0.326040
! "HE2" "HP" 0 1 131072 15 1 -0.033580
! "HE3" "HP" 0 1 131072 16 1 -0.033580
! "NZ" "N3" 0 1 131072 17 7 -1.035810
! "HZ2" "H" 0 1 131072 18 1 0.386040
! "HZ3" "H" 0 1 131072 19 1 0.386040
! "C" "C" 0 1 131072 20 6 0.597300
! "O" "O" 0 1 131072 21 8 -0.567900
!entry.LYN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"N" "N" 0 -1 0.0
"H" "H" 0 -1 0.0
--- 2121,2147 ----
0.0 0.0 0.0
0.0 0.0 0.0
!entry.LYN.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
! "N" "N" 0 1 131072 1 7 -0.453388
! "H" "H" 0 1 131072 2 1 0.289695
! "CA" "CT" 0 1 131072 3 6 -0.024500
! "HA" "H1" 0 1 131072 4 1 0.099553
! "CB" "CT" 0 1 131072 5 6 0.035478
! "HB2" "HC" 0 1 131072 6 1 0.004797
! "HB3" "HC" 0 1 131072 7 1 0.004797
! "CG" "CT" 0 1 131072 8 6 -0.019962
! "HG2" "HC" 0 1 131072 9 1 -0.015610
! "HG3" "HC" 0 1 131072 10 1 -0.015610
! "CD" "CT" 0 1 131072 11 6 0.041105
! "HD2" "HC" 0 1 131072 12 1 0.008304
! "HD3" "HC" 0 1 131072 13 1 0.008304
! "CE" "CT" 0 1 131072 14 6 0.188382
! "HE2" "HP" 0 1 131072 15 1 0.016810
! "HE3" "HP" 0 1 131072 16 1 0.016810
! "NZ" "N3" 0 1 131072 17 7 -0.894254
! "HZ2" "H" 0 1 131072 18 1 0.332053
! "HZ3" "H" 0 1 131072 19 1 0.332053
! "C" "C" 0 1 131072 20 6 0.608464
! "O" "O" 0 1 131072 21 8 -0.563281
!entry.LYN.unit.atomspertinfo table str pname str ptype int ptypex int pelmnt dbl pchg
"N" "N" 0 -1 0.0
"H" "H" 0 -1 0.0
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Temporary workarounds: none.