********>Bugfix 28:
Author: Junmei Wang and Anthony Fejes
Date: 12/10/2004
Programs: antechamber (gaff.dat file)
Description: There were some copy-and-paste errors leading to duplicate
and erroneous entries, plus a few parameters that referred to
non-existent atom types.
Fix: apply the following patch to amber8/dat/leap/parm/gaff.dat
------------------------------------------------------------------------------
*** gaff.dat 2003/11/13 23:51:07 1.12
--- gaff.dat 2004/12/10 17:58:26
***************
*** 163,169 ****
c1-na 452.0 1.362 SOURCE3 8 0.0031 0.0034
c1-ne 741.8 1.220 SOURCE3 1 0.0000 0.0000
c1-nf 741.8 1.220 SOURCE3 1 same as c1-ne
- c1-ng 465.7 1.353 SOURCE3 3 0.0025 0.0027
c1-nh 465.7 1.353 SOURCE3 3 0.0025 0.0027
c1-no 393.0 1.405 SOURCE3 3 0.0004 0.0005
c1-o 777.0 1.166 SOURCE2 9 0.0044 0.0052
--- 163,168 ----
***************
*** 333,339 ****
cc-pd 318.2 1.733 SOURCE3 84 same as cd-pc
cc-ss 279.3 1.737 SOURCE3 52 0.0162 0.0194
cd-cd 418.3 1.429 SOURCE1 740 0.0058 0.0069
- cd-cd 504.0 1.371 SOURCE3 523 same as cc-cd
cd-ce 519.2 1.362 SOURCE3 1 same as cc-cf
cd-cg 420.9 1.427 SOURCE1 560 0.0000 0.0000
cd-ch 420.9 1.427 SOURCE1 560 0.0000 0.0000
--- 332,337 ----
***************
*** 368,374 ****
ce-sx 239.7 1.797 SOURCE3 5 0.0080 0.0082
ce-sy 248.9 1.782 SOURCE3 5 0.0105 0.0114
cf-cf 390.5 1.451 SOURCE1 66 0.0060 0.0060
- cf-cf 562.4 1.338 SOURCE1 543 same as ce-cf
cf-cg 415.6 1.431 SOURCE1 22 0.0000 0.0000
cf-ch 415.6 1.431 SOURCE1 22 0.0000 0.0000
cf-ha 341.5 1.089 SOURCE3 55 0.0030 0.0056
--- 366,371 ----
***************
*** 389,395 ****
cg-ne 450.5 1.363 SOURCE3 4 0.0189 0.0204
cg-pe 429.8 1.621 SOURCE3 11 0.1928 0.2008
ch-ch 494.2 1.377 SOURCE1 42 0.0000 0.0000
- ch-ch 949.5 1.191 SOURCE1 80 same as cg-ch
ch-n1 994.7 1.143 SOURCE1 316 0.0011 0.0018
ch-nf 450.5 1.363 SOURCE3 4 same as cg-ne
ch-pf 429.8 1.621 SOURCE3 11 same as cg-pe
--- 386,391 ----
***************
*** 538,544 ****
n -sh 273.6 1.728 SOURCE3 4 0.0108 0.0128
n -ss 281.6 1.717 SOURCE3 7 0.0120 0.0133
n1-n1 1221.7 1.124 SOURCE1 19 0.0000 0.0000
- n1-n1 1365.7 1.100 SOURCE3
n1-n2 857.4 1.216 SOURCE1 19 0.0000 0.0000
n1-n3 535.7 1.350 SOURCE0 1
n1-n4 518.2 1.360 SOURCE0 1
--- 534,539 ----
***************
*** 650,656 ****
nc-ss 433.5 1.560 SOURCE1 74 0.0000 0.0000
nc-sy 439.8 1.555 SOURCE3 2
nd-nd 486.8 1.379 SOURCE3 9 0.0145 0.0164
- nd-nd 602.9 1.315 SOURCE3 9 same as nc-nd
nd-os 414.9 1.395 SOURCE1 46 0.0163 0.0188
nd-ss 433.5 1.560 SOURCE1 74 0.0000 0.0000
nd-sy 439.8 1.555 SOURCE3 2
--- 645,650 ----
***************
*** 665,671 ****
ne-sx 207.3 1.838 SOURCE3 7 0.0760 0.1060
ne-sy 257.1 1.752 SOURCE3 7 0.0640 0.0814
nf-nf 355.3 1.479 SOURCE3 19 same as ne-ne
- nf-nf 738.6 1.257 SOURCE3 1 same as ne-nf
nf-o 736.4 1.228 SOURCE3 40 same as ne- o
nf-p2 493.9 1.563 SOURCE3 14 same as ne-p2
nf-pf 327.8 1.712 SOURCE3 28 same as ne-pe
--- 659,664 ----
***************
*** 786,792 ****
pe-sx 145.9 2.168 SOURCE3 9 0.1092 0.1743
pe-sy 133.0 2.213 SOURCE3 6 0.0106 0.0127
pf-pf 240.7 2.092 SOURCE3 7 same as pe-pe
- pf-pf 260.8 2.055 SOURCE3 1 same as pe-pf
pf-px 291.4 2.005 SOURCE3 12 same as pe-px
pf-py 278.6 2.025 SOURCE3 12 same as pe-py
pf-s 374.7 1.758 SOURCE3 31 same as pe- s
--- 779,784 ----
***************
*** 4224,4230 ****
c1-n1-o 62.6 179.95 HF/6-31G*
c1-n1-oh 62.9 174.31 HF/6-31G*
c1-n1-os 62.2 176.61 HF/6-31G*
! c1-n1-p1 83.5 172.83 HF/6-31G*
c1-n1-p3 68.7 173.51 HF/6-31G*
c1-n1-p4 68.7 173.64 HF/6-31G*
c1-n1-p5 71.5 177.28 HF/6-31G*
--- 4216,4222 ----
c1-n1-o 62.6 179.95 HF/6-31G*
c1-n1-oh 62.9 174.31 HF/6-31G*
c1-n1-os 62.2 176.61 HF/6-31G*
! c1-n1-p2 83.5 172.83 HF/6-31G*
c1-n1-p3 68.7 173.51 HF/6-31G*
c1-n1-p4 68.7 173.64 HF/6-31G*
c1-n1-p5 71.5 177.28 HF/6-31G*
***************
*** 4234,4240 ****
c1-n1-s6 61.8 175.92 HF/6-31G*
c1-n1-sh 55.7 174.25 HF/6-31G*
c1-n1-ss 55.4 176.06 HF/6-31G*
- c1-ng-ng 51.9 179.97 HF/6-31G*
c2-c1-n1 63.1 180.00 HF/6-31G*
c2-c2-n1 71.7 122.98 HF/6-31G*
c2-n1-n1 61.6 180.00 HF/6-31G*
--- 4226,4231 ----
***************
*** 4272,4278 ****
n1-n1-os 64.0 176.12 HF/6-31G*
n1-n1-p2 69.4 174.71 HF/6-31G*
n1-n1-p3 70.2 174.27 HF/6-31G*
- n1-n1-s 54.6 179.96 HF/6-31G*
n1-n1-sh 57.0 175.07 HF/6-31G*
n1-n1-ss 56.9 175.61 HF/6-31G*
n1-p4-o 49.7 114.59 HF/6-31G*
--- 4263,4268 ----
***************
*** 4280,4286 ****
n1-s2-o 73.1 108.46 HF/6-31G*
n1-s4-o 70.2 110.09 HF/6-31G*
n1-s6-o 78.8 107.52 HF/6-31G*
- n1-c1-n1 70.2 180.00 HF/6-31G*
n1-c2-n1 73.6 124.15 HF/6-31G*
n1-c3-n1 80.0 105.07 HF/6-31G*
n1-ca-n1 75.8 117.03 HF/6-31G*
--- 4270,4275 ----
***************
*** 4323,4330 ****
nh-c1-nh 59.0 180.00 Guess
no-c1-no 56.8 180.00 Guess
na-c1-na 58.6 180.00 Guess
- na-c1-na 58.6 180.00 Guess
- na-c1-na 58.6 180.00 Guess
X -c -c -X 4 1.200 180.000 2.000
X -c -c1-X 2 0.000 180.000 2.000
--- 4312,4317 ----
***************
*** 4889,4895 ****
X -p3-py-X 6 11.000 180.000 2.000
X -p3-sh-X 2 9.200 0.000 2.000
X -p3-ss-X 2 2.300 0.000 3.000
- X -p3-ss-X 2 2.300 0.000 3.000
X -p3-s4-X 4 15.400 0.000 2.000
X -p3-sx-X 4 15.400 0.000 2.000
X -p3-s6-X 6 1.600 0.000 3.000
--- 4876,4881 ----
***************
*** 5038,5044 ****
c -c3-n -o 1.1 180. 2. Junmei et al.1999
c2-c2-na-c3 1.1 180. 2.
c2-c -c2-c3 1.1 180. 2.
- c3-o -c -oh 1.1 180. 2.
c2-c3-c2-hc 1.1 180. 2. Junmei et al.1999
c2-c3-ca-hc 1.1 180. 2. Junmei et al.1999
c2-hc-c -o 1.1 180. 2. Junmei et al.1999
--- 5024,5029 ----
***************
*** 5061,5075 ****
hc-o -c -oh 1.1 180. 2. Junmei et al.1999
hc-o -c -os 1.1 180. 2.
n2-c2-ca-n2 1.1 180. 2. dac guess, 9/94
- n2-ca-ca-c3 1.1 180. 2.
n2-ca-ca-n2 1.1 180. 2. dac guess, 9/94
- na-ca-ca-c3 1.1 180. 2.
na-n2-ca-n2 1.1 180. 2. dac, 10/94
X -X -X -X 1.1 180. 2. dac, 10/94
hw ow 0000. 0000. 4. flag for fast water
- n na n2
MOD4 RE
h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
--- 5046,5057 ----
----------------------------------------------------------------------------
Temporary workaround: none.