27 |
|
// sulfone |
28 |
|
SYZ 32.0655 |
29 |
|
// O in sulfone |
30 |
< |
OY |
30 |
> |
//OY |
31 |
|
// thiol S |
32 |
|
SH 32.0655 |
33 |
|
//Thiol H |
34 |
|
HS 1.0079 |
35 |
+ |
//Thiol S |
36 |
+ |
S 32.0655 |
37 |
|
// Sulfoxide |
38 |
|
SZ 32.0655 |
39 |
|
// Sulfur in disulfide |
115 |
|
SH 0.4610 3.62 |
116 |
|
SS 0.3279 3.72 |
117 |
|
SP 0.3576 3.60 |
118 |
+ |
// ---- End From TraPPE-UA |
119 |
|
end LennardJonesAtomTypes |
120 |
|
|
121 |
|
begin SCAtomTypes |
241 |
|
CH2 CH Harmonic 1.526 260 |
242 |
|
CH CH Harmonic 1.526 260 |
243 |
|
// fix the Kb for the thiol below: |
244 |
< |
S CH2 Harmonic 1.82 281 |
244 |
> |
S CH2 Harmonic 1.82 281 |
245 |
> |
SH CH2 Harmonic 1.82 281 |
246 |
|
|
247 |
|
//Atom1 Atom2 Cubic b0 K3 K2 K1 K0 |
248 |
|
//V_Cubic = K3(b - b0)^3 + K2(b - b0)^2 + K1(b - b0) + K0 |
267 |
|
//Theta0: degrees |
268 |
|
//Harmonic examples |
269 |
|
// |
270 |
< |
CH3 CH2 CH3 Harmonic 114.0 117.68 |
271 |
< |
CH3 CH2 CH2 Harmonic 114.0 117.68 |
272 |
< |
CH3 CH2 CH Harmonic 114.0 117.68 |
273 |
< |
CH3 CH CH3 Harmonic 112.0 117.68 |
274 |
< |
CH3 CH CH2 Harmonic 112.0 117.68 |
275 |
< |
CH3 CH CH Harmonic 112.0 117.68 |
276 |
< |
CH2 CH2 CH2 Harmonic 114.0 117.68 |
277 |
< |
CH2 CH2 CH Harmonic 114.0 117.68 |
270 |
> |
//CH3 CH2 CH3 Harmonic 114.0 117.68 |
271 |
> |
//CH3 CH2 CH2 Harmonic 114.0 117.68 |
272 |
> |
//CH3 CH2 CH Harmonic 114.0 117.68 |
273 |
> |
//CH3 CH CH3 Harmonic 112.0 117.68 |
274 |
> |
//CH3 CH CH2 Harmonic 112.0 117.68 |
275 |
> |
//CH3 CH CH Harmonic 112.0 117.68 |
276 |
> |
//CH2 CH2 CH2 Harmonic 114.0 117.68 |
277 |
> |
//CH2 CH2 CH Harmonic 114.0 117.68 |
278 |
|
CH2 CH CH2 Harmonic 112.0 117.68 |
279 |
|
CH2 CH CH Harmonic 112.0 117.68 |
280 |
< |
CH CH2 CH Harmonic 114.0 117.68 |
280 |
> |
//CH CH2 CH Harmonic 114.0 117.68 |
281 |
|
CH CH CH Harmonic 112.0 117.68 |
282 |
< |
S CH2 CH2 Harmonic 114.0 117.68 |
282 |
> |
|
283 |
> |
//From Lubna et al.JPCB 109, 24100 (2005) TraPPE |
284 |
> |
CH3 CH2 SH Harmonic 96.0 67.220 |
285 |
> |
CH2 CH2 SH Harmonic 96.0 67.220 |
286 |
> |
CH2 CH2 S Harmonic 114.0 124.19 |
287 |
> |
CH3 CH2 S Harmonic 114.0 124.19 |
288 |
> |
CH3 CH2 CH3 Harmonic 114.0 124.19 |
289 |
> |
CH3 CH2 CH2 Harmonic 114.0 124.19 |
290 |
> |
CH2 CH2 CH2 Harmonic 114.0 124.19 |
291 |
> |
CH3 CH2 CH Harmonic 114.0 124.19 |
292 |
> |
|
293 |
|
|
294 |
|
|
295 |
|
//UreyBradley |
384 |
|
//Atom1 Atom2 Atom3 Atom4 Cubic k3 k2 k1 k0 ( all are kcal/mol ) |
385 |
|
//V_Cubic = k3(cos phi)^3 + k2(cos phi)^2 + k1(cos phi) + k0 |
386 |
|
//Cubic Examples |
387 |
< |
CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
387 |
> |
//CH3 CH2 CH2 CH3 Cubic 5.9602 -0.2568 -3.802 2.1586 |
388 |
|
CH3 CH2 CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
389 |
|
CH3 CH CH CH3 Cubic 3.3254 -0.4215 -1.686 1.1661 |
390 |
< |
CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
390 |
> |
//CH3 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
391 |
|
CH3 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
392 |
|
CH3 CH CH2 CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
393 |
|
CH3 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
394 |
< |
CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
394 |
> |
//CH3 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
395 |
|
CH3 CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
396 |
|
CH3 CH CH2 CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
397 |
|
CH3 CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
398 |
< |
CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
398 |
> |
//CH2 CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
399 |
|
CH2 CH2 CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
400 |
|
CH2 CH CH CH2 Cubic 3.3254 -0.4215 -1.686 1.1661 |
401 |
|
CH2 CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
405 |
|
CH CH2 CH2 CH Cubic 5.9602 -0.2568 -3.802 2.1586 |
406 |
|
CH CH2 CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
407 |
|
CH CH CH CH Cubic 3.3254 -0.4215 -1.686 1.1661 |
408 |
< |
S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
408 |
> |
//S CH2 CH2 CH2 Cubic 5.9602 -0.2568 -3.802 2.1586 |
409 |
|
|
410 |
|
//Opls |
411 |
|
//Atom1 Atom2 Atom3 Atom4 Opls v1 v2 v3 |
412 |
|
//V_Opls = v1 / 2 * [1 + cos(phi)] + v2 / 2 * [1 - cos(2*phi)] + v3 / 2 * [1 + cos(3*phi)] |
413 |
|
//units for v_n: kcal / mol |
414 |
|
|
415 |
+ |
|
416 |
|
//Trappe |
417 |
|
//Atom1 Atom2 Atom3 Atom4 Trappe c0 c1 c2 c3 |
418 |
|
//V_Opls = c0 + c1 * [1 + cos(phi)] + c2 * [1 - cos(2*phi)] + c3 * [1 + cos(3*phi)] |
419 |
|
//units for c_n: kcal / mol |
420 |
|
|
421 |
+ |
//From Martin et al. JPCB 120, 2569 (1998) |
422 |
+ |
CH3 CH2 CH2 CH3 Trappe 0.0 0.70544 -0.13549 1.5723 |
423 |
+ |
CH3 CH2 CH2 CH2 Trappe 0.0 0.70544 -0.13549 1.5723 |
424 |
+ |
CH3 CH2 CH2 CH Trappe 0.0 0.70544 -0.13549 1.5723 |
425 |
+ |
CH2 CH2 CH2 CH2 Trappe 0.0 0.70544 -0.13549 1.5723 |
426 |
+ |
|
427 |
+ |
|
428 |
+ |
//From Lubna et al.JPCB 109, 24100 (2005) |
429 |
+ |
CH3 CH2 CH2 SH Trappe 0.10507 -0.10342 0.036680 0.60874 |
430 |
+ |
CH2 CH2 CH2 SH Trappe 0.10507 -0.10342 0.036680 0.60874 |
431 |
+ |
CH3 CH2 S CH2 Trappe 0.0 0.73041 -0.53685 1.1557 |
432 |
+ |
CH2 CH2 S CH2 Trappe 0.0 0.73041 -0.53685 1.1557 |
433 |
+ |
CH CH2 S CH2 Trappe 0.0 0.73041 -0.53685 1.1557 |
434 |
+ |
CH2 S S CH2 Trappe 3.5049 0.79083 -4.3348 1.003932 |
435 |
+ |
CH3 S S CH3 Trappe 3.5049 0.79083 -4.3348 1.003932 |
436 |
+ |
CH3 CH2 CH S Trappe -0.49886 0.85189 -0.22225 0.87680 |
437 |
+ |
CH3 CH2 CH S Trappe -0.49886 0.85189 -0.22225 0.87680 |
438 |
+ |
CH2 CH2 CH S Trappe -0.49886 0.85189 -0.22225 0.87680 |
439 |
+ |
CH CH2 CH S Trappe -0.49886 0.85189 -0.22225 0.87680 |
440 |
+ |
CH3 CH2 C S Trappe 0.0 0.0 0.0 0.91658 |
441 |
+ |
CH2 CH2 C S Trappe 0.0 0.0 0.0 0.91658 |
442 |
+ |
CH CH2 C S Trappe 0.0 0.0 0.0 0.91658 |
443 |
+ |
CH3 CG S H Trappe 0.0 0.0 0.0 0.79480 |
444 |
+ |
|
445 |
|
//Charmm |
446 |
|
//Atom1 Atom2 Atom3 Atom4 Charmm Kchi n delta [Kchi n delta] |
447 |
|
//V_Charmm = Kchi(1 + cos(n(chi) - delta)) |
458 |
|
//Atom1 Atom2 Atom3 Atom4 Polynomial i Ki [j Kj] |
459 |
|
//VPolynomial = Ki (cos phi)^i + ... + Kj (cos phi)^j |
460 |
|
|
461 |
+ |
|
462 |
|
end TorsionTypes |
463 |
|
|
464 |
|
|