204 |
|
CH2 CH2 Harmonic 1.526 260 |
205 |
|
CH2 CH Harmonic 1.526 260 |
206 |
|
CH CH Harmonic 1.526 260 |
207 |
+ |
// fix the Kb for the thiol below: |
208 |
|
S CH2 Harmonic 1.82 260 |
209 |
|
|
210 |
|
//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
268 |
|
end BendTypes |
269 |
|
|
270 |
|
begin TorsionTypes |
271 |
+ |
|
272 |
+ |
// All thiol torsions from Kautman and Klein (J. Phys. Chem. 1989, 91, 4994-5001) |
273 |
+ |
|
274 |
+ |
S CH2 CH2 CH3 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
275 |
+ |
S CH2 CH2 CH2 Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
276 |
+ |
S CH2 CH2 CH Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
277 |
+ |
S CH2 CH2 C Polynomial 0 2.218 1 2.905 2 -3.136 3 -0.7313 4 6.272 5 -7.528 |
278 |
+ |
|
279 |
+ |
// All type 1 possibilities from Dubbeldam et al. (J. Phys. Chem. B 2004, 108, 12301-12313) |
280 |
+ |
|
281 |
+ |
CH3 CH2 CH2 CH3 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
282 |
+ |
CH3 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
283 |
+ |
CH3 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
284 |
+ |
CH3 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
285 |
+ |
CH2 CH2 CH2 CH2 Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
286 |
+ |
CH2 CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
287 |
+ |
CH2 CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
288 |
+ |
CH CH2 CH2 CH Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
289 |
+ |
CH CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
290 |
+ |
C CH2 CH2 C Polynomial 0 2.3939 1 3.871 2 -0.7111 3 -3.864 4 1.4222 5 -3.111 |
291 |
+ |
|
292 |
+ |
// All type 2 possibilities: |
293 |
+ |
|
294 |
+ |
H CH CH2 CH3 Polynomial 0 2.7167 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
295 |
+ |
H CH CH2 CH2 Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
296 |
+ |
H CH CH2 CH Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
297 |
+ |
H CH CH2 C Polynomial 0 2.7161 1 8.665 2 0.82669 3 -12.92 4 -1.653 5 3.2712 |
298 |
|
|
299 |
+ |
// All type 3 possibilities: |
300 |
+ |
|
301 |
+ |
CH3 C CH2 CH3 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
302 |
+ |
CH3 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
303 |
+ |
CH3 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
304 |
+ |
CH3 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
305 |
+ |
CH2 C CH2 CH2 Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
306 |
+ |
CH2 C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
307 |
+ |
CH2 C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
308 |
+ |
CH C CH2 CH Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
309 |
+ |
CH C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
310 |
+ |
C C CH2 C Polynomial 0 2.5701 1 7.710 2 0 3 -10.29 4 0 5 0 |
311 |
+ |
|
312 |
+ |
// All type 4 possibilities: |
313 |
+ |
|
314 |
+ |
CH3 C C CH3 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
315 |
+ |
CH3 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
316 |
+ |
CH3 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
317 |
+ |
CH3 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
318 |
+ |
CH2 C C CH2 Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
319 |
+ |
CH2 C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
320 |
+ |
CH2 C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
321 |
+ |
CH C C CH Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
322 |
+ |
CH C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
323 |
+ |
C C C C Polynomial 0 4.0652 1 12.20 2 0 3 -16.26 4 0 5 0 |
324 |
+ |
|
325 |
+ |
//All type 5 possibilities: |
326 |
+ |
|
327 |
+ |
CH3 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
328 |
+ |
CH2 C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
329 |
+ |
CH C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
330 |
+ |
C C CH H Polynomial 0 3.1301 1 9.390 2 0 3 -12.52 4 0 5 0 |
331 |
+ |
|
332 |
+ |
//All type 6 possibilities: |
333 |
+ |
|
334 |
+ |
H CH CH H Polynomial 0 2.1706 1 5.609 2 -1.804 3 -5.976 4 3.6089 5 -3.6089 |
335 |
+ |
|
336 |
|
//Cubic |
337 |
|
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
338 |
|
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
339 |
|
//Cubic Examples |
340 |
< |
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
341 |
< |
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
342 |
< |
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
343 |
< |
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
344 |
< |
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
345 |
< |
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
346 |
< |
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
347 |
< |
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
348 |
< |
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
349 |
< |
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
350 |
< |
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
351 |
< |
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
352 |
< |
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
353 |
< |
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
354 |
< |
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
355 |
< |
CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
356 |
< |
CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
357 |
< |
CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
358 |
< |
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
359 |
< |
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
360 |
< |
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
361 |
< |
S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
340 |
> |
//CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
341 |
> |
//CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
342 |
> |
//CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
343 |
> |
//CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
344 |
> |
//CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
345 |
> |
//CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
346 |
> |
//CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
347 |
> |
//CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
348 |
> |
//CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
349 |
> |
//CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
350 |
> |
//CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
351 |
> |
//CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
352 |
> |
//CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
353 |
> |
//CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
354 |
> |
//CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
355 |
> |
//CH2 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
356 |
> |
//CH2 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
357 |
> |
//CH2 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
358 |
> |
//CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
359 |
> |
//CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
360 |
> |
//CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
361 |
> |
//S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
362 |
|
|
363 |
|
//Charmm |
364 |
|
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |