1PARM94 for DNA, RNA and proteins with TIP3P Water. USE SCEE=1.2 in energy progs
2BR 79.90                !            bromine
3C  12.01                             sp2 C carbonyl group
4CA 12.01                             sp2 C pure aromatic (benzene)
5CB 12.01                             sp2 aromatic C, 5&6 membered ring junction
6CC 12.01                             sp2 aromatic C, 5 memb. ring HIS
7CK 12.01                             sp2 C 5 memb.ring in purines
8CM 12.01                             sp2 C  pyrimidines in pos. 5 & 6
9CN 12.01                             sp2 C aromatic 5&6 memb.ring junct.(TRP)
10CQ 12.01                             sp2 C in 5 mem.ring of purines between 2 N
11CR 12.01                             sp2 arom as CQ but in HIS
12CT 12.01                             sp3 aliphatic C
13CV 12.01                             sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
14CW 12.01                             sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
15C* 12.01                             sp2 arom. 5 memb.ring w/1 subst. (TRP)
16C0 40.08                             calcium
17F  19.00                             fluorine
18H  1.008                             H bonded to nitrogen atoms
19HC 1.008                             H aliph. bond. to C without electrwd.group
20H1 1.008                             H aliph. bond. to C with 1 electrwd. group
21H2 1.008                             H aliph. bond. to C with 2 electrwd.groups
22H3 1.008                             H aliph. bond. to C with 3 eletrwd.groups
23HA 1.008                             H arom. bond. to C without elctrwd. groups
24H4 1.008                             H arom. bond. to C with 1 electrwd. group
25H5 1.008                             H arom. bond. to C with 2 electrwd. groups
26HO 1.008                             hydroxyl group
27HS 1.008                             hydrogen bonded to sulphur
28HW 1.008                             H in TIP3P water
29HP 1.008                             H bonded to C next to positively charged gr
30I  126.9                             iodine
31IM 35.45                             assumed to be Cl-
32IP 22.99                             assumed to be Na+
33IB 131.0                             'big ion w/ waters' for vacuum (Na+, 6H2O)
34MG 24.305                            magnesium
35N  14.01                             sp2 nitrogen in amide groups
36NA 14.01                             sp2 N in 5 memb.ring w/H atom (HIS)
37NB 14.01                             sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
38NC 14.01                             sp2 N in 6 memb.ring w/LP (ADE,GUA)
39N2 14.01                             sp2 N in amino groups
40N3 14.01                             sp3 N for charged amino groups (Lys, etc)
41N* 14.01                             sp2 N
42O  16.00                             carbonyl group oxygen
43OW 16.00                             oxygen in TIP3P water
44OH 16.00                             oxygen in hydroxyl group
45OS 16.00                             ether and ester oxygen
46O2 16.00                             carboxyl and phosphate group oxygen
47P  30.97                             phosphate
48S  32.06                             sulphur in disulfide linkage
49SH 32.06                             sulphur in cystine
50CU 63.55                             copper
51FE 55.00                             iron
52Li  6.94                             lithium
53K  39.10                             potassium
54Rb 85.47                             rubidium
55Cs 132.91                            cesium
56
57C   H   HO  N   NA  NB  NC  N2  NT  N2  N3  N*  O   OH  OS  P   O2
58OW-HW  553.0    0.9572    ! TIP3P water
59HW-HW  553.0    1.5136      TIP3P water
60C -CA  469.0    1.409       JCC,7,(1986),230; TYR
61C -CB  447.0    1.419       JCC,7,(1986),230; GUA
62C -CM  410.0    1.444       JCC,7,(1986),230; THY,URA
63C -CT  317.0    1.522       JCC,7,(1986),230; AA
64C -N*  424.0    1.383       JCC,7,(1986),230; CYT,URA
65C -NA  418.0    1.388       JCC,7,(1986),230; GUA.URA
66C -NC  457.0    1.358       JCC,7,(1986),230; CYT
67C -O   570.0    1.229       JCC,7,(1986),230; AA,CYT,GUA,THY,URA
68C -O2  656.0    1.250       JCC,7,(1986),230; GLU,ASP
69C -OH  450.0    1.364       JCC,7,(1986),230; TYR
70CA-CA  469.0    1.400       JCC,7,(1986),230; BENZENE,PHE,TRP,TYR
71CA-CB  469.0    1.404       JCC,7,(1986),230; ADE,TRP
72CA-CM  427.0    1.433       JCC,7,(1986),230; CYT
73CA-CT  317.0    1.510       JCC,7,(1986),230; PHE,TYR
74CA-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; PHE,TRP,TYR
75CA-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; no assigned
76CA-N2  481.0    1.340       JCC,7,(1986),230; ARG,CYT,GUA
77CA-NA  427.0    1.381       JCC,7,(1986),230; GUA
78CA-NC  483.0    1.339       JCC,7,(1986),230; ADE,CYT,GUA
79CB-CB  520.0    1.370       JCC,7,(1986),230; ADE,GUA
80CB-N*  436.0    1.374       JCC,7,(1986),230; ADE,GUA
81CB-NB  414.0    1.391       JCC,7,(1986),230; ADE,GUA
82CB-NC  461.0    1.354       JCC,7,(1986),230; ADE,GUA
83CK-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE,GUA
84CK-N*  440.0    1.371       JCC,7,(1986),230; ADE,GUA
85CK-NB  529.0    1.304       JCC,7,(1986),230; ADE,GUA
86CM-CM  549.0    1.350       JCC,7,(1986),230; CYT,THY,URA
87CM-CT  317.0    1.510       JCC,7,(1986),230; THY
88CM-HA  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
89CM-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; CYT,URA
90CM-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; not assigned
91CM-N*  448.0    1.365       JCC,7,(1986),230; CYT,THY,URA
92CQ-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes; ADE
93CQ-NC  502.0    1.324       JCC,7,(1986),230; ADE
94CT-CT  310.0    1.526       JCC,7,(1986),230; AA, SUGARS
95CT-HC  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, SUGARS
96CT-H1  340.0    1.090       changed from 331 bsd on NMA nmodes; AA, RIBOSE
97CT-H2  340.0    1.090       changed from 331 bsd on NMA nmodes; SUGARS
98CT-H3  340.0    1.090       changed from 331 bsd on NMA nmodes; not assigned
99CT-HP  340.0    1.090        changed from 331; AA-lysine, methyl ammonium cation
100CT-N*  337.0    1.475       JCC,7,(1986),230; ADE,CYT,GUA,THY,URA
101CT-N2  337.0    1.463       JCC,7,(1986),230; ARG
102CT-OH  320.0    1.410       JCC,7,(1986),230; SUGARS
103CT-OS  320.0    1.410       JCC,7,(1986),230; NUCLEIC ACIDS
104H -N2  434.0    1.010       JCC,7,(1986),230; ADE,CYT,GUA,ARG
105H -N*  434.0    1.010       for plain unmethylated bases ADE,CYT,GUA,ARG
106H -NA  434.0    1.010       JCC,7,(1986),230; GUA,URA,HIS
107HO-OH  553.0    0.960       JCC,7,(1986),230; SUGARS,SER,TYR
108HO-OS  553.0    0.960       JCC,7,(1986),230; NUCLEOTIDE ENDS
109O2-P   525.0    1.480       JCC,7,(1986),230; NA PHOSPHATES
110OH-P   230.0    1.610       JCC,7,(1986),230; NA PHOSPHATES
111OS-P   230.0    1.610       JCC,7,(1986),230; NA PHOSPHATES
112C*-HC  367.0    1.080       changed from 340. bsd on C6H6 nmodes, not needed AA
113C -N   490.0    1.335       JCC,7,(1986),230; AA
114C*-CB  388.0    1.459       JCC,7,(1986),230; TRP
115C*-CT  317.0    1.495       JCC,7,(1986),230; TRP
116C*-CW  546.0    1.352       JCC,7,(1986),230; TRP
117CA-CN  469.0    1.400       JCC,7,(1986),230; TRP
118CB-CN  447.0    1.419       JCC,7,(1986),230; TRP
119CC-CT  317.0    1.504       JCC,7,(1986),230; HIS
120CC-CV  512.0    1.375       JCC,7,(1986),230; HIS(delta)
121CC-CW  518.0    1.371       JCC,7,(1986),230; HIS(epsilon)
122CC-NA  422.0    1.385       JCC,7,(1986),230; HIS
123CC-NB  410.0    1.394       JCC,7,(1986),230; HIS
124CN-NA  428.0    1.380       JCC,7,(1986),230; TRP
125CR-H5  367.0    1.080       changed from 340. bsd on C6H6 nmodes;HIS
126CR-NA  477.0    1.343       JCC,7,(1986),230; HIS
127CR-NB  488.0    1.335       JCC,7,(1986),230; HIS
128CT-N   337.0    1.449       JCC,7,(1986),230; AA
129CT-N3  367.0    1.471       JCC,7,(1986),230; LYS
130CT-S   227.0    1.810       changed from 222.0 based on dimethylS nmodes
131CT-SH  237.0    1.810       changed from 222.0 based on methanethiol nmodes
132CV-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes; HIS
133CV-NB  410.0    1.394       JCC,7,(1986),230; HIS
134CW-H4  367.0    1.080       changed from 340. bsd on C6H6 nmodes;HIS(epsilon,+)
135CW-NA  427.0    1.381       JCC,7,(1986),230; HIS,TRP
136H -N   434.0    1.010       JCC,7,(1986),230; AA
137H -N3  434.0    1.010       JCC,7,(1986),230; LYS
138HS-SH  274.0    1.336       JCC,7,(1986),230; CYS
139S -S   166.0    2.038       JCC,7,(1986),230; CYX   (SCHERAGA)
140CT-F   367.0    1.380       JCC,13,(1992),963;CF4; R0=1.332 FOR CHF3
141
142HW-OW-HW    100.      104.52    TIP3P water
143HW-HW-OW      0.      127.74    (found in crystallographic water with 3 bonds)
144CB-C -NA    70.0      111.30    NA
145CB-C -O     80.0      128.80
146CM-C -NA    70.0      114.10
147CM-C -O     80.0      125.30
148CT-C -O     80.0      120.40
149CT-C -O2    70.0      117.00
150CT-C -OH    70.0      117.00
151N*-C -NA    70.0      115.40
152N*-C -NC    70.0      118.60
153N*-C -O     80.0      120.90
154NA-C -O     80.0      120.60
155NC-C -O     80.0      122.50
156CT-C -N     70.0      116.60    AA general
157N -C -O     80.0      122.90    AA general
158O -C -O     80.0      126.00    AA COO- terminal residues
159O2-C -O2    80.0      126.00    AA GLU            (SCH JPC 79,2379)
160O -C -OH    80.0      126.00
161CA-C -CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes; AA tyr
162CA-C -OH    70.0      120.00    AA tyr
163C -CA-CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
164CA-CA-CA    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
165CA-CA-CB    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes
166CA-CA-CT    70.0      120.00
167CA-CA-HA    35.0      120.00
168CA-CA-H4    35.0      120.00
169CB-CA-HA    35.0      120.00
170CB-CA-H4    35.0      120.00
171CB-CA-N2    70.0      123.50
172CB-CA-NC    70.0      117.30
173CM-CA-N2    70.0      120.10
174CM-CA-NC    70.0      121.50
175N2-CA-NA    70.0      116.00
176N2-CA-NC    70.0      119.30
177NA-CA-NC    70.0      123.30
178C -CA-HA    35.0      120.00    AA tyr
179N2-CA-N2    70.0      120.00    AA arg
180CN-CA-HA    35.0      120.00    AA trp
181CA-CA-CN    63.0      120.00    changed from 85.0  bsd on C6H6 nmodes; AA trp
182C -CB-CB    63.0      119.20    changed from 85.0  bsd on C6H6 nmodes; NA gua
183C -CB-NB    70.0      130.00
184CA-CB-CB    63.0      117.30    changed from 85.0  bsd on C6H6 nmodes; NA ade
185CA-CB-NB    70.0      132.40
186CB-CB-N*    70.0      106.20
187CB-CB-NB    70.0      110.40
188CB-CB-NC    70.0      127.70
189N*-CB-NC    70.0      126.20
190C*-CB-CA    63.0      134.90    changed from 85.0  bsd on C6H6 nmodes; AA trp
191C*-CB-CN    63.0      108.80    changed from 85.0  bsd on C6H6 nmodes; AA trp
192CA-CB-CN    63.0      116.20    changed from 85.0  bsd on C6H6 nmodes; AA trp
193H5-CK-N*    35.0      123.05
194H5-CK-NB    35.0      123.05
195N*-CK-NB    70.0      113.90
196C -CM-CM    63.0      120.70    changed from 85.0  bsd on C6H6 nmodes; NA thy
197C -CM-CT    70.0      119.70
198C -CM-HA    35.0      119.70
199C -CM-H4    35.0      119.70
200CA-CM-CM    63.0      117.00    changed from 85.0  bsd on C6H6 nmodes; NA cyt
201CA-CM-HA    35.0      123.30
202CA-CM-H4    35.0      123.30
203CM-CM-CT    70.0      119.70
204CM-CM-HA    35.0      119.70
205CM-CM-H4    35.0      119.70
206CM-CM-N*    70.0      121.20
207H4-CM-N*    35.0      119.10
208H5-CQ-NC    35.0      115.45
209NC-CQ-NC    70.0      129.10
210CM-CT-HC    50.0      109.50    changed based on NMA nmodes
211CT-CT-CT    40.0      109.50
212CT-CT-HC    50.0      109.50    changed based on NMA nmodes
213CT-CT-H1    50.0      109.50    changed based on NMA nmodes
214CT-CT-H2    50.0      109.50    changed based on NMA nmodes
215CT-CT-HP    50.0      109.50    changed based on NMA nmodes
216CT-CT-N*    50.0      109.50
217CT-CT-OH    50.0      109.50
218CT-CT-OS    50.0      109.50
219HC-CT-HC    35.0      109.50
220H1-CT-H1    35.0      109.50
221HP-CT-HP    35.0      109.50    AA lys, ch3nh4+
222H2-CT-N*    50.0      109.50    changed based on NMA nmodes
223H1-CT-N*    50.0      109.50    changed based on NMA nmodes
224H1-CT-OH    50.0      109.50    changed based on NMA nmodes
225H1-CT-OS    50.0      109.50    changed based on NMA nmodes
226H2-CT-OS    50.0      109.50    changed based on NMA nmodes
227N*-CT-OS    50.0      109.50
228H1-CT-N     50.0      109.50    AA general  changed based on NMA nmodes
229C -CT-H1    50.0      109.50    AA general  changed based on NMA nmodes
230C -CT-HP    50.0      109.50    AA zwitterion  changed based on NMA nmodes
231H1-CT-S     50.0      109.50    AA cys     changed based on NMA nmodes
232H1-CT-SH    50.0      109.50    AA cyx     changed based on NMA nmodes
233CT-CT-S     50.0      114.70    AA cyx            (SCHERAGA  JPC 79,1428)
234CT-CT-SH    50.0      108.60    AA cys
235H2-CT-H2    35.0      109.50    AA lys
236H1-CT-N2    50.0      109.50    AA arg     changed based on NMA nmodes
237HP-CT-N3    50.0      109.50    AA lys, ch3nh3+, changed based on NMA nmodes
238CA-CT-CT    63.0      114.00    AA phe tyr          (SCH JPC  79,2379)
239C -CT-HC    50.0      109.50    AA gln      changed based on NMA nmodes
240C -CT-N     63.0      110.10    AA general
241CT-CT-N2    80.0      111.20    AA arg             (JCP 76, 1439)
242CT-CT-N     80.0      109.70    AA ala, general    (JACS 94, 2657)
243C -CT-CT    63.0      111.10    AA general
244CA-CT-HC    50.0      109.50    AA tyr     changed based on NMA nmodes
245CT-CT-N3    80.0      111.20    AA lys             (JCP 76, 1439)
246CC-CT-CT    63.0      113.10    AA his
247CC-CT-HC    50.0      109.50    AA his     changed based on NMA nmodes
248C -CT-N3    80.0      111.20    AA amino terminal residues
249C*-CT-CT    63.0      115.60    AA trp
250C*-CT-HC    50.0      109.50    AA trp    changed based on NMA nmodes
251CT-CC-NA    70.0      120.00    AA his
252CT-CC-CV    70.0      120.00    AA his
253CT-CC-NB    70.0      120.00    AA his
254CV-CC-NA    70.0      120.00    AA his
255CW-CC-NA    70.0      120.00    AA his
256CW-CC-NB    70.0      120.00    AA his
257CT-CC-CW    70.0      120.00    AA his
258H5-CR-NA    35.0      120.00    AA his
259H5-CR-NB    35.0      120.00    AA his
260NA-CR-NA    70.0      120.00    AA his
261NA-CR-NB    70.0      120.00    AA his
262CC-CV-H4    35.0      120.00    AA his
263CC-CV-NB    70.0      120.00    AA his
264H4-CV-NB    35.0      120.00    AA his
265CC-CW-H4    35.0      120.00    AA his
266CC-CW-NA    70.0      120.00    AA his
267H4-CW-NA    35.0      120.00    AA his
268C*-CW-H4    35.0      120.00    AA trp
269C*-CW-NA    70.0      108.70    AA trp
270CT-C*-CW    70.0      125.00    AA trp
271CB-C*-CT    70.0      128.60    AA trp
272CB-C*-CW    63.0      106.40    changed from 85.0  bsd on C6H6 nmodes; AA trp
273CA-CN-NA    70.0      132.80    AA trp
274CB-CN-NA    70.0      104.40    AA trp
275CA-CN-CB    63.0      122.70    changed from 85.0  bsd on C6H6 nmodes; AA trp
276C -N -CT    50.0      121.90    AA general
277C -N -H     30.0      120.00    AA general, gln, asn,changed based on NMA nmodes
278CT-N -H     30.0      118.04    AA general,     changed based on NMA nmodes
279CT-N -CT    50.0      118.00    AA pro             (DETAR JACS 99,1232)
280H -N -H     35.0      120.00    ade,cyt,gua,gln,asn     **
281C -N*-CM    70.0      121.60
282C -N*-CT    70.0      117.60
283C -N*-H     30.0      119.20    changed based on NMA nmodes
284CB-N*-CK    70.0      105.40
285CB-N*-CT    70.0      125.80
286CB-N*-H     30.0      125.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
287CK-N*-CT    70.0      128.80
288CK-N*-H     30.0      128.80    for unmethylated n.a. bases,chngd bsd NMA nmodes
289CM-N*-CT    70.0      121.20
290CM-N*-H     30.0      121.20    for unmethylated n.a. bases,chngd bsd NMA nmodes
291CA-N2-H     35.0      120.00
292H -N2-H     35.0      120.00
293CT-N2-H     35.0      118.40    AA arg
294CA-N2-CT    50.0      123.20    AA arg
295CT-N3-H     50.0      109.50    AA lys,     changed based on NMA nmodes
296CT-N3-CT    50.0      109.50    AA pro/nt
297H -N3-H     35.0      109.50    AA lys, AA(end)
298C -NA-C     70.0      126.40
299C -NA-CA    70.0      125.20
300C -NA-H     30.0      116.80    changed based on NMA nmodes
301CA-NA-H     30.0      118.00    changed based on NMA nmodes
302CC-NA-CR    70.0      120.00    AA his
303CC-NA-H     30.0      120.00    AA his,    changed based on NMA nmodes
304CR-NA-CW    70.0      120.00    AA his
305CR-NA-H     30.0      120.00    AA his,    changed based on NMA nmodes
306CW-NA-H     30.0      120.00    AA his,    changed based on NMA nmodes
307CN-NA-CW    70.0      111.60    AA trp
308CN-NA-H     30.0      123.10    AA trp,    changed based on NMA nmodes
309CB-NB-CK    70.0      103.80
310CC-NB-CR    70.0      117.00    AA his
311CR-NB-CV    70.0      117.00    AA his
312C -NC-CA    70.0      120.50
313CA-NC-CB    70.0      112.20
314CA-NC-CQ    70.0      118.60
315CB-NC-CQ    70.0      111.00
316C -OH-HO    35.0      113.00
317CT-OH-HO    55.0      108.50
318HO-OH-P     45.0      108.50
319CT-OS-CT    60.0      109.50
320CT-OS-P    100.0      120.50
321P -OS-P    100.0      120.50
322O2-P -OH    45.0      108.23
323O2-P -O2   140.0      119.90
324O2-P -OS   100.0      108.23
325OH-P -OS    45.0      102.60
326OS-P -OS    45.0      102.60
327CT-S -CT    62.0       98.90    AA met
328CT-S -S     68.0      103.70    AA cyx             (SCHERAGA  JPC 79,1428)
329CT-SH-HS    43.0       96.00    changed from 44.0 based on methanethiol nmodes
330HS-SH-HS    35.0       92.07    AA cys
331F -CT-F     77.0      109.10    JCC,13,(1992),963;
332F -CT-H1    35.0      109.50    JCC,13,(1992),963;
333
334X -C -CA-X    4   14.50        180.0             2.         intrpol.bsd.on C6H6
335X -C -CB-X    4   12.00        180.0             2.         intrpol.bsd.on C6H6
336X -C -CM-X    4    8.70        180.0             2.         intrpol.bsd.on C6H6
337X -C -N*-X    4    5.80        180.0             2.         JCC,7,(1986),230
338X -C -NA-X    4    5.40        180.0             2.         JCC,7,(1986),230
339X -C -NC-X    2    8.00        180.0             2.         JCC,7,(1986),230
340X -C -OH-X    2    1.80        180.0             2.         JCC,7,(1986),230
341X -C -CT-X    4    0.00          0.0             2.         JCC,7,(1986),230
342X -CA-CA-X    4   14.50        180.0             2.         intrpol.bsd.on C6H6
343X -CA-CB-X    4   14.00        180.0             2.         intrpol.bsd.on C6H6
344X -CA-CM-X    4   10.20        180.0             2.         intrpol.bsd.on C6H6
345X -CA-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
346X -CA-N2-X    4    9.60        180.0             2.         reinterpolated 93'
347X -CA-NA-X    4    6.00        180.0             2.         JCC,7,(1986),230
348X -CA-NC-X    2    9.60        180.0             2.         JCC,7,(1986),230
349X -CB-CB-X    4   21.80        180.0             2.         intrpol.bsd.on C6H6
350X -CB-N*-X    4    6.60        180.0             2.         JCC,7,(1986),230
351X -CB-NB-X    2    5.10        180.0             2.         JCC,7,(1986),230
352X -CB-NC-X    2    8.30        180.0             2.         JCC,7,(1986),230
353X -CK-N*-X    4    6.80        180.0             2.         JCC,7,(1986),230
354X -CK-NB-X    2   20.00        180.0             2.         JCC,7,(1986),230
355X -CM-CM-X    4   26.60        180.0             2.         intrpol.bsd.on C6H6
356X -CM-CT-X    6    0.00          0.0             3.         JCC,7,(1986),230
357X -CM-N*-X    4    7.40        180.0             2.         JCC,7,(1986),230
358X -CQ-NC-X    2   13.60        180.0             2.         JCC,7,(1986),230
359X -CT-CT-X    9    1.40          0.0             3.         JCC,7,(1986),230
360X -CT-N -X    6    0.00          0.0             2.         JCC,7,(1986),230
361X -CT-N*-X    6    0.00          0.0             2.         JCC,7,(1986),230
362X -CT-N2-X    6    0.00          0.0             3.         JCC,7,(1986),230
363X -CT-OH-X    3    0.50          0.0             3.         JCC,7,(1986),230
364X -CT-OS-X    3    1.15          0.0             3.         JCC,7,(1986),230
365X -OH-P -X    3    0.75          0.0             3.         JCC,7,(1986),230
366X -OS-P -X    3    0.75          0.0             3.         JCC,7,(1986),230
367X -C -N -X    4   10.00        180.0             2.         AA|check Wendy?&NMA
368X -CT-N3-X    9    1.40          0.0             3.         JCC,7,(1986),230
369X -CT-S -X    3    1.00          0.0             3.         JCC,7,(1986),230
370X -CT-SH-X    3    0.75          0.0             3.         JCC,7,(1986),230
371X -C*-CB-X    4    6.70        180.0             2.         intrpol.bsd.onC6H6aa
372X -C*-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
373X -C*-CW-X    4   26.10        180.0             2.         intrpol.bsd.on C6H6
374X -CA-CN-X    4   14.50        180.0             2.         reinterpolated 93'
375X -CB-CN-X    4   12.00        180.0             2.         reinterpolated 93'
376X -CC-CT-X    6    0.00          0.0             2.         JCC,7,(1986),230
377X -CC-CV-X    4   20.60        180.0             2.         intrpol.bsd.on C6H6
378X -CC-CW-X    4   21.50        180.0             2.         intrpol.bsd.on C6H6
379X -CC-NA-X    4    5.60        180.0             2.         JCC,7,(1986),230
380X -CC-NB-X    2    4.80        180.0             2.         JCC,7,(1986),230
381X -CN-NA-X    4    6.10        180.0             2.         reinterpolated 93'
382X -CR-NA-X    4    9.30        180.0             2.         JCC,7,(1986),230
383X -CR-NB-X    2   10.00        180.0             2.         JCC,7,(1986),230
384X -CV-NB-X    2    4.80        180.0             2.         JCC,7,(1986),230
385X -CW-NA-X    4    6.00        180.0             2.         JCC,7,(1986),230
386CT-CT-OS-CT   1    0.383         0.0            -3.
387CT-CT-OS-CT   1    0.1         180.0             2.
388C -N -CT-C    1    0.20        180.0             2.
389N -CT-C -N    1    0.40        180.0            -4.
390N -CT-C -N    1    1.35        180.0            -2.
391N -CT-C -N    1    0.75        180.0             1.
392CT-CT-N -C    1    0.50        180.0            -4.
393CT-CT-N -C    1    0.15        180.0            -3.
394CT-CT-N -C    1    0.53          0.0             1.
395CT-CT-C -N    1    0.100         0.0            -4.
396CT-CT-C -N    1    0.07          0.0             2.
397H -N -C -O    1    2.50        180.0            -2.         JCC,7,(1986),230
398H -N -C -O    1    2.00          0.0             1.         J.C.cistrans-NMA DE
399CT-S -S -CT   1    3.50          0.0            -2.         JCC,7,(1986),230
400CT-S -S -CT   1    0.60          0.0             3.         JCC,7,(1986),230
401OS-CT-CT-OS   1    0.144         0.0            -3.         JCC,7,(1986),230
402OS-CT-CT-OS   1    1.00          0.0             2.         pucker anal (93')
403OS-CT-CT-OH   1    0.144         0.0            -3.         JCC,7,(1986),230
404OS-CT-CT-OH   1    1.00          0.0             2.         pucker anal (93')
405OH-CT-CT-OH   1    0.144         0.0            -3.         JCC,7,(1986),230
406OH-CT-CT-OH   1    1.00          0.0             2.         check glicolWC? puc
407OH-P -OS-CT   1    0.25          0.0            -3.         JCC,7,(1986),230
408OH-P -OS-CT   1    1.20          0.0             2.         gg&gt ene.631g*/mp2
409OS-P -OS-CT   1    0.25          0.0            -3.         JCC,7,(1986),230
410OS-P -OS-CT   1    1.20          0.0             2.         gg&gt ene.631g*/mp2
411OS-CT-N*-CK   1    0.50        180.0            -2.         sugar frag calc (PC)
412OS-CT-N*-CK   1    2.50          0.0             1.         sugar frag calc (PC)
413OS-CT-N*-CM   1    0.50        180.0            -2.         sugar frag calc (PC)
414OS-CT-N*-CM   1    2.50          0.0             1.         sugar frag calc (PC)
415
416X -X -C -O          10.5         180.          2.           JCC,7,(1986),230
417X -O2-C -O2         10.5         180.          2.           JCC,7,(1986),230
418X -X -N -H          1.0          180.          2.           JCC,7,(1986),230
419X -X -N2-H          1.0          180.          2.           JCC,7,(1986),230
420X -X -NA-H          1.0          180.          2.           JCC,7,(1986),230
421X -N2-CA-N2         10.5         180.          2.           JCC,7,(1986),230
422X -CT-N -CT         1.0          180.          2.           JCC,7,(1986),230
423X -X -CA-HA         1.1          180.          2.           bsd.on C6H6 nmodes
424X -X -CW-H4         1.1          180.          2.
425X -X -CR-H5         1.1          180.          2.
426X -X -CV-H4         1.1          180.          2.
427X -X -CQ-H5         1.1          180.          2.
428X -X -CK-H5         1.1          180.          2.
429X -X -CM-H4         1.1          180.          2.
430X -X -CM-HA         1.1          180.          2.
431X -X -CA-H4         1.1          180.          2.           bsd.on C6H6 nmodes
432X -X -CA-H5         1.1          180.          2.           bsd.on C6H6 nmodes
433CK-CB-N*-CT         1.0          180.          2.
434CM-C -N*-CT         1.0          180.          2.           dac guess, 9/94
435CM-C -CM-CT         1.1          180.          2.
436CT-O -C -OH         10.5         180.          2.
437NA-CV-CC-CT         1.1          180.          2.
438NB-CW-CC-CT         1.1          180.          2.
439NA-CW-CC-CT         1.1          180.          2.
440CW-CB-C*-CT         1.1          180.          2.
441CA-CA-CA-CT         1.1          180.          2.
442C -CM-CM-CT         1.1          180.          2.           dac guess, 9/94
443NC-CM-CA-N2         1.1          180.          2.           dac guess, 9/94
444CB-NC-CA-N2         1.1          180.          2.           dac, 10/94
445NA-NC-CA-N2         1.1          180.          2.           dac, 10/94
446CA-CA-C -OH         1.1          180.          2.
447
448  HW  OW  0000.     0000.                                4.  flag for fast water
449
450N   NA  N2  N*  NC  NB  N3  NP  NO
451C   C*  CA  CB  CC  CN  CM  CK  CQ  CW  CV  CR  CA  CX  CY  CD
452
453MOD4      RE
454  H           0.6000  0.0157            !Ferguson base pair geom.
455  HO          0.0000  0.0000             OPLS Jorgensen, JACS,110,(1988),1657
456  HS          0.6000  0.0157             W. Cornell CH3SH --> CH3OH FEP
457  HC          1.4870  0.0157             OPLS
458  H1          1.3870  0.0157             Veenstra et al JCC,8,(1992),963
459  H2          1.2870  0.0157             Veenstra et al JCC,8,(1992),963
460  H3          1.1870  0.0157             Veenstra et al JCC,8,(1992),963
461  HP          1.1000  0.0157             Veenstra et al JCC,8,(1992),963
462  HA          1.4590  0.0150             Spellmeyer
463  H4          1.4090  0.0150             Spellmeyer, one electrowithdr. neighbor
464  H5          1.3590  0.0150             Spellmeyer, two electrowithdr. neighbor
465  HW          0.0000  0.0000             TIP3P water model
466  O           1.6612  0.2100             OPLS
467  O2          1.6612  0.2100             OPLS
468  OW          1.7683  0.1520             TIP3P water model
469  OH          1.7210  0.2104             OPLS
470  OS          1.6837  0.1700             OPLS ether
471  CT          1.9080  0.1094             Spellmeyer
472  CA          1.9080  0.0860             Spellmeyer
473  CM          1.9080  0.0860             Spellmeyer
474  C           1.9080  0.0860             OPLS
475  N           1.8240  0.1700             OPLS
476  S           2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
477  SH          2.0000  0.2500             W. Cornell CH3SH and CH3SCH3 FEP's
478  P           2.1000  0.2000             JCC,7,(1986),230;
479  IM          2.47    0.1                Cl- Smith & Dang, JCP 1994,100:5,3757
480  Li          1.1370  0.0183             Li+ Aqvist JPC 1990,94,8021. (adapted)
481  IP          1.8680  0.00277            Na+ Aqvist JPC 1990,94,8021. (adapted)
482  K           2.6580  0.000328           K+  Aqvist JPC 1990,94,8021. (adapted)
483  Rb          2.9560  0.00017            Rb+ Aqvist JPC 1990,94,8021. (adapted)
484  Cs          3.3950  0.0000806          Cs+ Aqvist JPC 1990,94,8021. (adapted)
485  I           2.35    0.40               JCC,7,(1986),230;
486  F           1.75    0.061              Gough et al. JCC 13,(1992),963.
487  IB          5.0     0.1                solvated ion for vacuum approximation
488
489END
490END
491